I would assume it would upgrade to F, but will probably post as F/_ where F is fare flown and _ is the fare you paid for. Mileage is based on the latter, so unless you were flying on a B or higher fare, you'll only get 100% EQM.

This is just like elite upgrades, which post as R/_ or F/_ depending on whether EUA upgraded you or you were upgraded at checkin (I've had two segments recently miss EUA but upgrade to F when I checked in online).