Losing temple upgrades (limps) for no reason

Happened to me like three times now in two days.
Temple upgrades for hands and feet sometimes just disappear when I use “respawn at checkpoint” inside the temple.

Maybe it has something to do with using the respawn option when I accidentally enter the architect chamber. Instead of fighting him and destroying my temple, I port out before the fight begins. Maybe the game counts that as me dying and therefore removes the upgrades?