Did you checkout the entire family table when you modified a few instances? This is critical for modifying a FT in Windchill. You should always checkout and modify the entire FT, not just a few instances. Do something simple, like add a dummy relation, verify the FT, then remove the relation and verify again to force the entire FT to be marked as modified so it can be checked back in.
Once you do this, you should be able to check in your assembly.
If you do not have access to change the FT, my users do not, then get with your WIndchill librarian to make the changes. We have Windchill set to mark all library files as read-only to the users so they cannot make changes.
You may need to undo the checkout of the FT from your workspace and lose the changes, but that may also allow the assemblies and drawings to be checked-in.
