(in version 126.96.36.1991)
Maybe you have this already handled in a newer release, but in case you don't:
When I am syncing a missing table into my database, it errors with "ORA-00955: name is already used by an existing object", because a synonym of that same name already exists. Deleting the synonym manually fixes this error.
The expected behavior, I think, would be to include the synonyms in the comparison window and have it show that one 1 side it is a table, and the other a synonym, and syncing would delete one before copying from the other.