since nobody has responded yet I'll take a stab,
you could try what you've suggested, I think gate agents should be able to change your FF# after you've checked in, though you might have a simpler time checking in with your AS # and flashing your AA credentials, charm, and good cheer at the manned check in counter to waive the bag fees. If that doesn't work, you could have them enter your AA number, legitimately waive your fees, and then try to switch back at the gate.