There's a trophy in Ratchet and Clank (2016) that requires you to hit every single enemy in the game with the Groovitron, a portable disco ball that forces enemies to dance while you blast them to smithereens. Anyway, this isn't sold in the store until you reach Rilgar, which is potentially after you have missed enemies for a certain playthrough. Does this trophy track across playthroughs? Or do you have to start all over again in challenge mode?
The answer is sort of.
On a normal New Game (i.e., non-challenge mode) playthrough that you then take into challenge mode by defeating the final boss and then selected 'challenge mode' on the title menu, it does track.
However, progress will be reset on all subsequent challenge mode starts. If you fail to receive the trophy in your first challenge mode playthrough, you will need to begin anew in your quest to make the enemies dance when you begin your second challenge mode playthrough (or third, fourth, etc.)
Here's a simpler breakdown:
New Game -> Challenge Mode (Progress is carried over)
Challenge Mode -> Challenge Mode (Progress is NOT carried over)