Hi,
It does not matter, the original booking class will still be credited (if it gets credited).
I have a few times upgraded my A3 flights with the upgrade coupon but credit them to TK, and no matter by which method (automatic or by manual request), the original booking class is credited.
So changing the FFP will only either just delay the credit process or a manual request is needed - because the upgraded class is not eligible.
Cheers!