Have you already tried doing a "recover" on the file with FMP12 after moving it over to it's new location? I'm not sure that rebuilding the field indexes would solve your problem, but if you do it on a copy it couldn't hurt.
From my talks with some other users in the past, the recommendation is to not tamper with the files at all, as it's pretty touchy on how it stores those references.
My only other thought would be to temporarily convert it back to in-database storage, move the file and rehost, then switch back to reference storage.
I think the best approach to move a solution that includes Remote Container data would be do use the admin console on the old server to download the solution (that packages the RC data properly), the use the new server's admin console to upload the solution (which again packages the RC data properly and puts it where FMS expects it).
What Wim said.
I thought there was some sort of way to convert the file back to store data internally/temporarily for a move.