Updating a FF number after booking is always "risky". From what I know, there are two fields in the system for FF... Don't ask which ones, I have no idea...
But you do have to make sure that BOTH fields are replaced by the FF number that you want to accrue to.
Best is to do that with a real person rather than a machine though.
Keep the physical BP, only send scans until they request for the original. But then keep a scan for yourself, you never know.
Good luck