Thank you for your post.
Since the import used to work, something has obviously changed.
First, find a subset of records in the current file, clone the file, open the clone, and import from the subset of records. Does this work? If so, then we know the current file is fine. If not, then the file may be corrupt. Remove the records from the clone file, close the file, and run Recover on the clone file. When finished, open the clone file and try the import again. If this works, then the corruption MAY have been fixed. I say "MAY" because FileMaker Pro does its best to fix a file. It is not a cure-all solution. The recommendation would be to find an old backup that works properly, or recreate the file.
If the importing of records into the clone was fine, then the problem may lie in the secondary file that you were importing from. In this case, you may just want to import the records into the Clone file and use that as your new secondary file.
Also, could there be multiple table instances in the source database, and the layout you are using for the found set is based on a different instance than the one you are trying to import?