I have no good ides but someone here may. I would use a rigid putty-knife about three inches wide to scrape the floor. At some point a drum sander can be brought in but not before a lot (if not most) of the thinset has been removed.
You could also try a scrubby pad type thing with a little water but don't allow the floor to get too wet and don't let any water get into the cracks between the boards. If you do that then also use a fan to dry the floor as soon as possible.