pre-tiling bathroom floor
I would let it set..... or you will warp the cement board as you squish the thin set.
Screw or nail it right now! The idea of the thinset , so when it is secured is to fill any and all voids .. If you wait to long the thinset may have to be scraped up and you start anew. Any questions you can e mail me through my avatar and check my qualifications there. GL