If a scene change via ISY didn't properly clean up link tables in insteon devices, is there a way to edit the table to manually remove links through ISY or do I have to factory reset all devices with the bad links?  I know ISY can display the link table but I don't see a way to force down changes.

If you select on the device, right click and pick "restore device". That should do it. For really stubborn devices, follow the devices factory reset steps first before restoring

In addition to @paulbates suggestion, no the link tables cannot be manually edited.

If you suspect the link tables are mismatched you can run a device link table diagnostic, then a compare. That will show if the controller link tables match those stored in the PLM. If there's a mismatch, then a restore device will rewrite the PLM link tables so they match those stored in the controller.