Transcedence only loses potential if you fail because you didn’t use enough gems to have 100% chance of success.
Refine usually goes first, if you can get your weapon to +11 or +16 (or higher, if you’re super lucky), then you can throw in transcedence. If you’re feeling lucky and weapon still has lots of potential left, you can risk 80%+ transcedence chance instead of 100% (but also risk losing potential there) and possibly save some gems (or not).
Personally I always go for 100% chance, so no possible potential loss.