This is the key point. The number of alternates reached the maximum number allowed so obviously you need to delete the AIX, redefine it with a larger record size, and then rebuild the AIX and path.This code is linked to 99 other codes via an alternate index which has reached it's currently defined maximum.
There is probably no easy way -- if any at all -- to reconcile the differences. The VSAM Demystified recbook explicitly states that the primary keys in an alternate index are kept in ascending sequence. However, since the current file is hitting the maximum number of keys allowed in an AIX record, there's no way to tell which record caused the maximum to be reached -- so rebuilding the AIX may cause differences since the primary keys will be loaded in ascending order, not in the order added to the base cluster. And since the whole purpose of rebuilding is to increase the record size for the alternate index, you cannot directly compare the old and new anyway -- since the new will have records with more than 99 primary keys and the old is limited to 99 primary keys.