I've done the "enter one FF# for status and another for miles" dance on LH with following procedure and it worked without any problems:
a) before check-in, change your FF# on PNR to the one where you have status
b) check-in, select seat, enjoy exit row if in Y
c) change FF# on PNR to the one where you want the miles to go
d) generate BPs again - they will have new FF#
I only use mobile BP in passbook and show the *G ones to lounge dragons - I scan the other one at the gate.
Dunno if half of this steps if irrelevant or redundant, but this has been working for me without any hitch.