I'm sorry, but as with the last tread, this is going to be a bit of advice for the future, rather than advice for now.
As you can see and have said, the bees are pretty good at clearing up the mess you make, so don't worry too much.
So, if you use a queen excluder, my advice would be that it was the last thing you removed before tucking the bees up for the winter.
Then you know the queen isn't likely to be anywhere other than in the brood box, whilst you are messing around upstairs.
If you don't use a QE, then yes, you have to expect that the queen could be anywhere in the hive and act appropriately.
As for the comb, I'm sorry, but I had assumed that you had removed all the broken pieces.
As you've realised, the bees will stick down anything that is loose.
I haven't had any comb in a 20mm eke, yet!
Just go carefully, checking for the queen.
And remove any new comb if necessary.
Oh, and don't twist, just in case!