diff --git a/dvc/remote/base.py b/dvc/remote/base.py
--- a/dvc/remote/base.py
+++ b/dvc/remote/base.py
@@ -592,6 +592,7 @@ def _checkout_file(
 
         self.link(cache_info, path_info)
         self.state.save_link(path_info)
+        self.state.save(path_info, checksum)
         if progress_callback:
             progress_callback.update(path_info.url)
 
@@ -613,22 +614,24 @@ def _checkout_dir(
         entry_info = copy(path_info)
         for entry in dir_info:
             relpath = entry[self.PARAM_RELPATH]
-            checksum = entry[self.PARAM_CHECKSUM]
-            entry_cache_info = self.checksum_to_path_info(checksum)
+            entry_checksum = entry[self.PARAM_CHECKSUM]
+            entry_cache_info = self.checksum_to_path_info(entry_checksum)
             entry_info.url = self.ospath.join(path_info.url, relpath)
             entry_info.path = self.ospath.join(path_info.path, relpath)
 
-            entry_checksum_info = {self.PARAM_CHECKSUM: checksum}
+            entry_checksum_info = {self.PARAM_CHECKSUM: entry_checksum}
             if self.changed(entry_info, entry_checksum_info):
                 if self.exists(entry_info):
                     self.safe_remove(entry_info, force=force)
                 self.link(entry_cache_info, entry_info)
+                self.state.save(entry_info, entry_checksum)
             if progress_callback:
                 progress_callback.update(entry_info.url)
 
         self._remove_redundant_files(path_info, dir_info, force)
 
         self.state.save_link(path_info)
+        self.state.save(path_info, checksum)
 
     def _remove_redundant_files(self, path_info, dir_info, force):
         existing_files = set(

Ok, can also confirm a similar thing for large data dirs. Looks like the issue is a common one:
```
#!/bin/bash                                   
                                              
set -e                                        
set -x                                        
                                              
rm -rf mytest                                 
mkdir mytest                                  
cd mytest                                     
                                              
REMOTE=$(pwd)/myremote                        
mkdir $REMOTE                                 
                                              
mkdir myrepo                                  
cd myrepo                                     
git init                                      
dvc init                                      
                                              
dvc remote add myremote $REMOTE -d            
                                              
mkdir data                                    
for f in {0..100}; do                         
        echo $f > data/$f                     
done                                          
                                              
#dd if=/dev/urandom of=data  bs=1M  count=1111
                                              
dvc add data                                  
                                              
dvc status                                    
                                              
dvc status                                    
                                              
dvc push                                      
                                              
rm -rf data                                   
rm -rf .dvc/cache                             
                                              
dvc status                                    
                                              
dvc pull                                      
                                              
dvc status                                    
                                              
dvc status                                    
```
And even more simple reproducer:
```
#!/bin/bash                                  
                                             
set -e                                       
set -x                                       
                                             
rm -rf mytest                                
mkdir mytest                                 
cd mytest                                    
                                                       
mkdir myrepo                                 
cd myrepo                                    
git init                                     
dvc init                                     
                                                                   
mkdir data                                   
for f in {0..100}; do                        
        echo $f > data/$f                    
done                                         
                                             
#dd if=/dev/urandom of=data  bs=1M  count=1111
                                             
dvc add data                                 
                                             
dvc status                                   
                                             
dvc status                                   
                                             
rm -rf data                                  
                                             
dvc status                                   
                                             
dvc checkout                                 
                                             
dvc status                                   
                                             
dvc status                                   
```

so `checkout` seems to be doing something to checksums that resets them.
diff --git a/tests/func/test_add.py b/tests/func/test_add.py
--- a/tests/func/test_add.py
+++ b/tests/func/test_add.py
@@ -268,6 +268,15 @@ def test(self):
             self.assertEqual(ret, 0)
             self.assertEqual(file_md5_counter.mock.call_count, 1)
 
+            os.rename(self.FOO, self.FOO + ".back")
+            ret = main(["checkout"])
+            self.assertEqual(ret, 0)
+            self.assertEqual(file_md5_counter.mock.call_count, 1)
+
+            ret = main(["status"])
+            self.assertEqual(ret, 0)
+            self.assertEqual(file_md5_counter.mock.call_count, 1)
+
 
 class TestShouldUpdateStateEntryForDirectoryAfterAdd(TestDvc):
     def test(self):
@@ -291,6 +300,15 @@ def test(self):
             self.assertEqual(ret, 0)
             self.assertEqual(file_md5_counter.mock.call_count, 3)
 
+            os.rename(self.DATA_DIR, self.DATA_DIR + ".back")
+            ret = main(["checkout"])
+            self.assertEqual(ret, 0)
+            self.assertEqual(file_md5_counter.mock.call_count, 3)
+
+            ret = main(["status"])
+            self.assertEqual(ret, 0)
+            self.assertEqual(file_md5_counter.mock.call_count, 3)
+
 
 class TestAddCommit(TestDvc):
     def test(self):

Re-compute of md5 for large files.
**Please provide information about your setup**
DVC v0.40.1, installed via Pipenv on Ubuntu 16.

See also #1659, which was a similar issue but for large directories.

It seems there is a bug which causes the md5 to be re-computed for large files.  @efiop was able to find a reproducible example for it.  From discord:

```bash
#!/bin/bash                                  
                                             
set -e                                       
set -x                                       
                                             
rm -rf mytest                                
mkdir mytest                                 
cd mytest                                    
                                             
REMOTE=$(pwd)/myremote                       
mkdir $REMOTE                                
                                             
mkdir myrepo                                 
cd myrepo                                    
git init                                     
dvc init                                     
                                             
dvc remote add myremote $REMOTE -d           
                                             
dd if=/dev/urandom of=data  bs=1M  count=1111
                                             
dvc add data                                 
                                             
dvc status                                   
                                             
dvc status                                   
                                             
dvc push                                     
                                             
rm -rf data                                  
rm -rf .dvc/cache                            
                                             
dvc status                                   
                                             
dvc pull                                     
                                             
dvc status                                   
                                             
dvc status                                   
```

> Even on pull it computes md5 of the same file twice. And then again on status after it once. Interesting.

tests/func/test_add.py::TestShouldUpdateStateEntryForFileAfterAdd::test tests/func/test_add.py::TestShouldUpdateStateEntryForDirectoryAfterAdd::test
tests/func/test_add.py::TestAddExternalLocalFile::test tests/func/test_add.py::TestAddDirectory::test tests/func/test_add.py::TestDoubleAddUnchanged::test_dir tests/func/test_add.py::TestShouldPlaceStageInDataDirIfRepositoryBelowSymlink::test tests/func/test_add.py::TestAddDirWithExistingCache::test tests/func/test_add.py::TestAddFileInDir::test tests/func/test_add.py::TestAddDirectoryRecursive::test tests/func/test_add.py::TestAdd::test tests/func/test_add.py::TestShouldCollectDirCacheOnlyOnce::test tests/func/test_add.py::TestShouldAddDataFromInternalSymlink::test tests/func/test_add.py::TestAddCommit::test tests/func/test_add.py::TestShouldCleanUpAfterFailedAdd::test tests/func/test_add.py::TestShouldThrowProperExceptionOnCorruptedStageFile::test tests/func/test_add.py::TestAddDirectoryWithForwardSlash::test tests/func/test_add.py::TestAddFilename::test tests/func/test_add.py::TestAdd::test_unicode tests/func/test_add.py::TestAddModifiedDir::test tests/func/test_add.py::TestAddUnupportedFile::test tests/func/test_add.py::TestShouldNotTrackGitInternalFiles::test tests/func/test_add.py::TestShouldAddDataFromExternalSymlink::test tests/func/test_add.py::TestCmdAdd::test tests/func/test_add.py::TestDoubleAddUnchanged::test_file tests/func/test_add.py::TestAddTrackedFile::test tests/func/test_add.py::TestShouldNotCheckCacheForDirIfCacheMetadataDidNotChange::test tests/func/test_add.py::TestAddCmdDirectoryRecursive::test tests/func/test_add.py::TestAddLocalRemoteFile::test