Partially? For me, it's always fully reset the count, so that's strange. Maybe check the Discord, the dedicated gamer discussions all happen there.
Could be the challenge mod nerfing level ups. Other than that, I don't know what could be causing differences.
Forgot to add this. The partially thing came from me leveling up after beating the first salaris encounter in the caverns I remember that my energy was full but arousal was left at around 30 ish. (I don't fully remember details)
I don't really remember wether I was. Also, I am not complaining, I am just trying to figure out what the difference between the difficulties are. Another thing, I have read what the challenge mod does. The effects of the challenge mod are optional. the effects are either, 1: double spirit loss, 2: immediate loss on spirit loss, 3: no sex skills, can only use the whip and other holy weapons, or 4: nothing.