diff --git a/stix2/markings/granular_markings.py b/stix2/markings/granular_markings.py
index be5d258..7c227d9 100644
--- a/stix2/markings/granular_markings.py
+++ b/stix2/markings/granular_markings.py
@@ -116,9 +116,9 @@ def remove_markings(obj, marking, selectors):
     granular_markings = utils.compress_markings(granular_markings)
 
     if granular_markings:
-        return new_version(obj, granular_markings=granular_markings)
+        return new_version(obj, granular_markings=granular_markings, allow_custom=True)
     else:
-        return new_version(obj, granular_markings=None)
+        return new_version(obj, granular_markings=None, allow_custom=True)
 
 
 def add_markings(obj, marking, selectors):
@@ -152,7 +152,7 @@ def add_markings(obj, marking, selectors):
 
     granular_marking = utils.expand_markings(granular_marking)
     granular_marking = utils.compress_markings(granular_marking)
-    return new_version(obj, granular_markings=granular_marking)
+    return new_version(obj, granular_markings=granular_marking, allow_custom=True)
 
 
 def clear_markings(obj, selectors):
@@ -207,9 +207,9 @@ def clear_markings(obj, selectors):
     granular_markings = utils.compress_markings(granular_markings)
 
     if granular_markings:
-        return new_version(obj, granular_markings=granular_markings)
+        return new_version(obj, granular_markings=granular_markings, allow_custom=True)
     else:
-        return new_version(obj, granular_markings=None)
+        return new_version(obj, granular_markings=None, allow_custom=True)
 
 
 def is_marked(obj, marking=None, selectors=None, inherited=False, descendants=False):
diff --git a/stix2/markings/object_markings.py b/stix2/markings/object_markings.py
index c0375c3..a169fe3 100644
--- a/stix2/markings/object_markings.py
+++ b/stix2/markings/object_markings.py
@@ -37,7 +37,7 @@ def add_markings(obj, marking):
 
     object_markings = set(obj.get("object_marking_refs", []) + marking)
 
-    return new_version(obj, object_marking_refs=list(object_markings))
+    return new_version(obj, object_marking_refs=list(object_markings), allow_custom=True)
 
 
 def remove_markings(obj, marking):
@@ -69,9 +69,9 @@ def remove_markings(obj, marking):
 
     new_markings = [x for x in object_markings if x not in marking]
     if new_markings:
-        return new_version(obj, object_marking_refs=new_markings)
+        return new_version(obj, object_marking_refs=new_markings, allow_custom=True)
     else:
-        return new_version(obj, object_marking_refs=None)
+        return new_version(obj, object_marking_refs=None, allow_custom=True)
 
 
 def set_markings(obj, marking):
@@ -103,7 +103,7 @@ def clear_markings(obj):
         A new version of the given SDO or SRO with object_marking_refs cleared.
 
     """
-    return new_version(obj, object_marking_refs=None)
+    return new_version(obj, object_marking_refs=None, allow_custom=True)
 
 
 def is_marked(obj, marking=None):
diff --git a/stix2/utils.py b/stix2/utils.py
index 73337d0..37ff166 100644
--- a/stix2/utils.py
+++ b/stix2/utils.py
@@ -251,7 +251,7 @@ def revoke(data):
 
     if data.get("revoked"):
         raise RevokeError("revoke")
-    return new_version(data, revoked=True)
+    return new_version(data, revoked=True, allow_custom=True)
 
 
 def get_class_hierarchy_names(obj):

Calling add_markings on a existing STIX object with custom properties causes an exception
Here is the stack trace:

Traceback (most recent call last):
 ```
 File "/Users/rpiazza/projects/capec-attack/capec2stix/capec2stix.py", line 197, in <module>
    main()
  File "/Users/rpiazza/projects/capec-attack/capec2stix/capec2stix.py", line 189, in main
    tlos = convert2stix(attack_pattern_catalog, marking_def.id, ident.id)
  File "/Users/rpiazza/projects/capec-attack/capec2stix/capec2stix.py", line 170, in convert2stix
    return convert_attack_pattern(attack_pattern_catalog.Attack_Patterns.Attack_Pattern[0],  marking_def_id, ident_id)
  File "/Users/rpiazza/projects/capec-attack/capec2stix/capec2stix.py", line 158, in convert_attack_pattern
    ap.add_markings(marking_def_id)
  File "/Users/rpiazza/py-envs/python3.5/lib/python3.5/site-packages/stix2/markings/__init__.py", line 143, in add_markings
    return object_markings.add_markings(obj, marking)
  File "/Users/rpiazza/py-envs/python3.5/lib/python3.5/site-packages/stix2/markings/object_markings.py", line 40, in add_markings
    return new_version(obj, object_marking_refs=list(object_markings))
  File "/Users/rpiazza/py-envs/python3.5/lib/python3.5/site-packages/stix2/utils.py", line 234, in new_version
    return cls(**{k: v for k, v in new_obj_inner.items() if v is not None})
  File "/Users/rpiazza/py-envs/python3.5/lib/python3.5/site-packages/stix2/base.py", line 111, in __init__
    raise ExtraPropertiesError(cls, extra_kwargs)
stix2.exceptions.ExtraPropertiesError: Unexpected properties for AttackPattern: (x_capec_abstraction, x_capec_consequences, x_capec_example_instances, x_capec_likelihood_of_attack, x_capec_prerequisites, x_capec_skills_required, x_capec_typical_severity, x_resources_required).
```
diff --git a/stix2/test/test_custom.py b/stix2/test/test_custom.py
index 7c1832b..76ad61b 100644
--- a/stix2/test/test_custom.py
+++ b/stix2/test/test_custom.py
@@ -2,7 +2,14 @@ import pytest
 
 import stix2
 
-from .constants import FAKE_TIME
+from .constants import FAKE_TIME, MARKING_DEFINITION_ID
+
+IDENTITY_CUSTOM_PROP = stix2.Identity(
+    name="John Smith",
+    identity_class="individual",
+    x_foo="bar",
+    allow_custom=True,
+)
 
 
 def test_identity_custom_property():
@@ -82,18 +89,38 @@ def test_parse_identity_custom_property(data):
 
 
 def test_custom_property_in_bundled_object():
-    identity = stix2.Identity(
-        name="John Smith",
-        identity_class="individual",
-        x_foo="bar",
-        allow_custom=True,
-    )
-    bundle = stix2.Bundle(identity, allow_custom=True)
+    bundle = stix2.Bundle(IDENTITY_CUSTOM_PROP, allow_custom=True)
 
     assert bundle.objects[0].x_foo == "bar"
     assert '"x_foo": "bar"' in str(bundle)
 
 
+def test_identity_custom_property_revoke():
+    identity = IDENTITY_CUSTOM_PROP.revoke()
+    assert identity.x_foo == "bar"
+
+
+def test_identity_custom_property_edit_markings():
+    marking_obj = stix2.MarkingDefinition(
+        id=MARKING_DEFINITION_ID,
+        definition_type="statement",
+        definition=stix2.StatementMarking(statement="Copyright 2016, Example Corp")
+    )
+    marking_obj2 = stix2.MarkingDefinition(
+        id=MARKING_DEFINITION_ID,
+        definition_type="statement",
+        definition=stix2.StatementMarking(statement="Another one")
+    )
+
+    # None of the following should throw exceptions
+    identity = IDENTITY_CUSTOM_PROP.add_markings(marking_obj)
+    identity2 = identity.add_markings(marking_obj2, ['x_foo'])
+    identity2.remove_markings(marking_obj.id)
+    identity2.remove_markings(marking_obj2.id, ['x_foo'])
+    identity2.clear_markings()
+    identity2.clear_markings('x_foo')
+
+
 def test_custom_marking_no_init_1():
     @stix2.CustomMarking('x-new-obj', [
         ('property1', stix2.properties.StringProperty(required=True)),

pip install -e .
parse_log_pytest
requirements.txt
pytest
3.6
requirements.txt
pytest --no-header -rA --tb=line --color=no -p no:cacheprovider -W ignore::DeprecationWarning
alabaster==0.7.13
antlr4-python3-runtime==4.9.3
async-generator==1.10
attrs==22.2.0
Babel==2.11.0
backcall==0.2.0
bleach==4.1.0
bump2version==1.0.1
bumpversion==0.6.0
certifi==2021.5.30
cfgv==3.3.1
charset-normalizer==2.0.12
coverage==6.2
decorator==5.1.1
defusedxml==0.7.1
distlib==0.3.9
docutils==0.18.1
entrypoints==0.4
filelock==3.4.1
identify==2.4.4
idna==3.10
imagesize==1.4.1
importlib-metadata==4.8.3
importlib-resources==5.2.3
iniconfig==1.1.1
ipython==7.16.3
ipython-genutils==0.2.0
jedi==0.17.2
Jinja2==3.0.3
jsonschema==3.2.0
jupyter-client==7.1.2
jupyter-core==4.9.2
jupyterlab-pygments==0.1.2
MarkupSafe==2.0.1
mistune==0.8.4
nbclient==0.5.9
nbconvert==6.0.7
nbformat==5.1.3
nbsphinx==0.8.8
nest-asyncio==1.6.0
nodeenv==1.6.0
packaging==21.3
pandocfilters==1.5.1
parso==0.7.1
pexpect==4.9.0
pickleshare==0.7.5
platformdirs==2.4.0
pluggy==1.0.0
pre-commit==2.17.0
prompt-toolkit==3.0.36
ptyprocess==0.7.0
py==1.11.0
Pygments==2.14.0
pyparsing==3.1.4
pyrsistent==0.18.0
pytest==7.0.1
pytest-cov==4.0.0
python-dateutil==2.9.0.post0
pytz==2025.2
PyYAML==6.0.1
pyzmq==25.1.2
requests==2.27.1
simplejson==3.20.1
six==1.17.0
snowballstemmer==2.2.0
Sphinx==5.3.0
sphinx-prompt==1.5.0
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-serializinghtml==1.1.5
-e git+https://github.com/oasis-open/cti-python-stix2.git@4a9c38e0b50415f4733072fc76eb8ebd0749c84b#egg=stix2
stix2-patterns==2.0.0
taxii2-client==2.3.0
testpath==0.6.0
toml==0.10.2
tomli==1.2.3
tornado==6.1
tox==3.28.0
traitlets==4.3.3
typing_extensions==4.1.1
urllib3==1.26.20
virtualenv==20.16.2
wcwidth==0.2.13
webencodings==0.5.1
zipp==3.6.0

name: cti-python-stix2
channels:
  - defaults
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
  - conda-forge
dependencies:
  - _libgcc_mutex=0.1=main
  - _openmp_mutex=5.1=1_gnu
  - ca-certificates=2025.2.25=h06a4308_0
  - certifi=2021.5.30=py36h06a4308_0
  - ld_impl_linux-64=2.40=h12ee557_0
  - libffi=3.3=he6710b0_2
  - libgcc-ng=11.2.0=h1234567_1
  - libgomp=11.2.0=h1234567_1
  - libstdcxx-ng=11.2.0=h1234567_1
  - ncurses=6.4=h6a678d5_0
  - openssl=1.1.1w=h7f8727e_0
  - pip=21.2.2=py36h06a4308_0
  - python=3.6.13=h12debd9_1
  - readline=8.2=h5eee18b_0
  - setuptools=58.0.4=py36h06a4308_0
  - sqlite=3.45.3=h5eee18b_0
  - tk=8.6.14=h39e8969_0
  - wheel=0.37.1=pyhd3eb1b0_0
  - xz=5.6.4=h5eee18b_1
  - zlib=1.2.13=h5eee18b_1
  - pip:
      - alabaster==0.7.13
      - antlr4-python3-runtime==4.9.3
      - async-generator==1.10
      - attrs==22.2.0
      - babel==2.11.0
      - backcall==0.2.0
      - bleach==4.1.0
      - bump2version==1.0.1
      - bumpversion==0.6.0
      - cfgv==3.3.1
      - charset-normalizer==2.0.12
      - coverage==6.2
      - decorator==5.1.1
      - defusedxml==0.7.1
      - distlib==0.3.9
      - docutils==0.18.1
      - entrypoints==0.4
      - filelock==3.4.1
      - identify==2.4.4
      - idna==3.10
      - imagesize==1.4.1
      - importlib-metadata==4.8.3
      - importlib-resources==5.2.3
      - iniconfig==1.1.1
      - ipython==7.16.3
      - ipython-genutils==0.2.0
      - jedi==0.17.2
      - jinja2==3.0.3
      - jsonschema==3.2.0
      - jupyter-client==7.1.2
      - jupyter-core==4.9.2
      - jupyterlab-pygments==0.1.2
      - markupsafe==2.0.1
      - mistune==0.8.4
      - nbclient==0.5.9
      - nbconvert==6.0.7
      - nbformat==5.1.3
      - nbsphinx==0.8.8
      - nest-asyncio==1.6.0
      - nodeenv==1.6.0
      - packaging==21.3
      - pandocfilters==1.5.1
      - parso==0.7.1
      - pexpect==4.9.0
      - pickleshare==0.7.5
      - platformdirs==2.4.0
      - pluggy==1.0.0
      - pre-commit==2.17.0
      - prompt-toolkit==3.0.36
      - ptyprocess==0.7.0
      - py==1.11.0
      - pygments==2.14.0
      - pyparsing==3.1.4
      - pyrsistent==0.18.0
      - pytest==7.0.1
      - pytest-cov==4.0.0
      - python-dateutil==2.9.0.post0
      - pytz==2025.2
      - pyyaml==6.0.1
      - pyzmq==25.1.2
      - requests==2.27.1
      - simplejson==3.20.1
      - six==1.17.0
      - snowballstemmer==2.2.0
      - sphinx==5.3.0
      - sphinx-prompt==1.5.0
      - sphinxcontrib-applehelp==1.0.2
      - sphinxcontrib-devhelp==1.0.2
      - sphinxcontrib-htmlhelp==2.0.0
      - sphinxcontrib-jsmath==1.0.1
      - sphinxcontrib-qthelp==1.0.3
      - sphinxcontrib-serializinghtml==1.1.5
      - stix2-patterns==2.0.0
      - taxii2-client==2.3.0
      - testpath==0.6.0
      - toml==0.10.2
      - tomli==1.2.3
      - tornado==6.1
      - tox==3.28.0
      - traitlets==4.3.3
      - typing-extensions==4.1.1
      - urllib3==1.26.20
      - virtualenv==20.16.2
      - wcwidth==0.2.13
      - webencodings==0.5.1
      - zipp==3.6.0
prefix: /opt/conda/envs/cti-python-stix2

stix2/test/test_custom.py::test_identity_custom_property_revoke stix2/test/test_custom.py::test_identity_custom_property_edit_markings
stix2/test/test_custom.py::test_identity_custom_property stix2/test/test_custom.py::test_identity_custom_property_invalid stix2/test/test_custom.py::test_identity_custom_property_allowed stix2/test/test_custom.py::test_parse_identity_custom_property[{\n stix2/test/test_custom.py::test_custom_property_in_bundled_object stix2/test/test_custom.py::test_custom_marking_no_init_1 stix2/test/test_custom.py::test_custom_marking_no_init_2 stix2/test/test_custom.py::test_custom_object_raises_exception stix2/test/test_custom.py::test_custom_object_type stix2/test/test_custom.py::test_custom_object_no_init_1 stix2/test/test_custom.py::test_custom_object_no_init_2 stix2/test/test_custom.py::test_parse_custom_object_type stix2/test/test_custom.py::test_parse_unregistered_custom_object_type stix2/test/test_custom.py::test_custom_observable_object_1 stix2/test/test_custom.py::test_custom_observable_object_2 stix2/test/test_custom.py::test_custom_observable_object_3 stix2/test/test_custom.py::test_custom_observable_raises_exception stix2/test/test_custom.py::test_custom_observable_object_no_init_1 stix2/test/test_custom.py::test_custom_observable_object_no_init_2 stix2/test/test_custom.py::test_custom_observable_object_invalid_ref_property stix2/test/test_custom.py::test_custom_observable_object_invalid_refs_property stix2/test/test_custom.py::test_custom_observable_object_invalid_refs_list_property stix2/test/test_custom.py::test_custom_observable_object_invalid_valid_refs stix2/test/test_custom.py::test_custom_no_properties_raises_exception stix2/test/test_custom.py::test_custom_wrong_properties_arg_raises_exception stix2/test/test_custom.py::test_parse_custom_observable_object stix2/test/test_custom.py::test_parse_unregistered_custom_observable_object stix2/test/test_custom.py::test_parse_invalid_custom_observable_object stix2/test/test_custom.py::test_observable_custom_property stix2/test/test_custom.py::test_observable_custom_property_invalid stix2/test/test_custom.py::test_observable_custom_property_allowed stix2/test/test_custom.py::test_observed_data_with_custom_observable_object stix2/test/test_custom.py::test_custom_extension_raises_exception stix2/test/test_custom.py::test_custom_extension stix2/test/test_custom.py::test_custom_extension_wrong_observable_type stix2/test/test_custom.py::test_custom_extension_invalid_observable stix2/test/test_custom.py::test_custom_extension_no_properties stix2/test/test_custom.py::test_custom_extension_empty_properties stix2/test/test_custom.py::test_custom_extension_no_init_1 stix2/test/test_custom.py::test_custom_extension_no_init_2 stix2/test/test_custom.py::test_parse_observable_with_custom_extension stix2/test/test_custom.py::test_parse_observable_with_unregistered_custom_extension stix2/test/test_custom.py::test_register_custom_object
stix2/utils.py stix2/markings/granular_markings.py stix2/markings/object_markings.py
stix2/utils.py stix2/markings/granular_markings.py stix2/markings/object_markings.py