I don’t think the film contains any answers to this question. However, concomitant with the crucifix rape scene, we are again reminded that paranormal powers are associated with demonic activity. Earlier there had been the noises in the attic and the bed-shaking. During the crucifix incident, there are now large-scale manifestations such as the “wind” that blows the curtains and throws the 45-RPM records around, plus the moving of furniture to block Chris’s exit from the room.
Perhaps we are meant to figure it out that the demon “levitated” the crucifix back upstairs to Regan’s room during Kinderman’s interview with Chris. That’s all I can come up with as an explanation of how the crucifix re-appeared in Regan’s room. The only other solution is that there were more than one crucifix in the house and one was hidden (maybe by Karl?) somewhere in Regan’s room – which is quite a stretch.