I've never had to work in 3.0, so take all backups before trying my advice :)
It sounds like you need to go to the layer files themselves to fix the issue.
Export your development.
Shut down the AOS.
Backup & delete your vap layer files and aoi file.
Start up the aos.
Determine what needs to be imported, and re-import from your export. But be
sure to import into the correct layer.
Oh, and you'll probably have to import without the id #'s. (Thus letting it
make new ids in the correct layer for your problem table).
Lots of testing ahead!
Tony Zeigler