You (as the controller of Progenitus) get to decide which replacement effect happens. After this first replacement effect happens, the remaining effect doesn't have anything to replace, because the "enters the graveyard" isn't part of the effect.
616.1. If two or more replacement and/or prevention effects are attempting to modify the way an event affects an object or player, the affected object's controller (or its owner if it has no controller) or the affected player chooses one to apply, following the steps listed below. If two or more players have to make these choices at the same time, choices are made in APNAP order (see rule 101.4).