If anything seems out of sync, the instructions in this post resolve it for most people:
If you have different setups for different covenants, you will probably want to activate each covenant in-game once and export, that will update the cache with information about soulbinds and conduits and renown levels for each of your covenants.
If you post a snapshot we can take a closer look at your case for this trinket, instructions on how to do that here:
One thing to possibly check is the max number of on-use items setting in the setup step.