The persister code "mints" a new OCFL id from a resource's "root" Fedora id when it creates a new resource rather than looking up what OCFL id is mapped to the "root" id. This fails if the OCFL id already associated to the root id is different than the id that the "minting" code generates.
This problem can be seen when F6 operates on AGs produced by the migration utils. The migration utils map Fedora ids to OCFL ids differently than F6 presently does. So, when F6 tries to add resources to migrated AGs, it actually inserts the new resources into the incorrect OCFL object.