Bennett,
With Sync tables you cannot change the key field after setting it up ( I know its ridiculous that you can't). You basically have to delete the connection, and re-create the sync. Your relationships should still be there, but you will have to reconnect the data to the appropriate fields.
If you have some scripts running you'll have to change the fids too.
Its nuts they haven't addressed this issue yet. for this reason we usually build a script that copies the sync, to a normal QB table, prior to actually connecting it to the database.
I've had to redo 2 different sync tables because the source data changed, its not fun
