All but one particular hotel chain (starts with 'H' and rhymes with 'diet') usually lets me keep the points, even when the folio is reversed.
From my understanding, it's a somewhat difficult process to remove the points, as opposed to the credit reversal. I'm guessing a hotel manager would not take the time to do it unless they really had an issue with the report or were required to.
Hotels that reimburse for the stay usually have no knowledge of who the shopper was, so I would think that one would always keep the points in that case. You also get the advantage of the credit card points with those stays, so they can be a good deal if you don't mind having the charges sit on your card for a while.
Another thing I have found it that cruises where you are gifted the ticket by the cruise line do not you keep the points for the cruise, sadly :^(
For each cruise I have evaluated, the points have been systematically removed from my account after the report was submitted.