What did it say in your reservation?

What counts (assuming you don't override at check-in) is the earning prefernce at the time you make the intiial reservation online, not the earning preference at any other time.

Then when you make the reservation, and also if you print out the reservation confirmation later, it should say somewhere on there "your Mileage Plus #blabla was used in this reservation".

In fact, once it's in the reservation there is no way (that I've found) to change it online, without cancelling and rebooking the reservation.

I don't see how the hotel could have changed it if you didn't show them your Choice card. That's because if your preference on the reservation is miles, there's no record of your Choice account number in the reservation! I've run into this (and documented it in a separate thread) where it came up that a property wasn't giving me (an Elite Diamond this year) my USA Today every morning because "we only give it to Choice Priveleges members" ("I am one"), "oh, we only have enough for Diamond" ("I am one"), "no, it says here you're AA" ("what?"), "it says you're AA" (and then reads off my AAdvantage number)!

However, in the past when I've had stays that I wanted to be miles post as points, I have been able to contact Choice customer service by email and get it corrected (including the 3x bonus), tho sometimes it took a while and some followup. (If instead something posts as miles and you wanted points, that's too late, because the miles have left the building by the time you can verify that's what happened.) I haven't had to do this for a couple years now so don't have any recent experience with this...