Oracle sqldeveloper Database Diff - not seeing indexes/sequences
This may not be an answer but worth to check up. Some indexes may have been set to invisible as an alternative to being dropped. These are still maintained by the database but ignored by the optimizer. You'll be able to see them by querying the dictionary, but the compare tool may ignore them.

SELECT INDEX_NAME, INDEX_TYPE, VISIBILITY
FROM ALL_INDEXES
WHERE INDEX_NAME LIKE 'EMP%';