Removing residual thinset and slight highspots in subfloor before another layer of plywood underlayerment
I had a similar problem and I just ran a three inch cold chisel over the areas that were a problem. Granted, you might not want to do a large area like this but for a small bathroom, it worked great. No thinset dust to breath, it just shaved the residue off the sub floor and I swept it up. Just a thought. You could use a regular chisel but you'd have to put a new edge on it afterwards.