I can say that this has not been my experience. I’ve got a set of LaBella flat wounds that I’ll rotate on and off one of my P Basses when needed, I believe I bought them somewhere around 12-13 years ago.
I do worry sometimes that the thinner part of the string that wraps around the tuning machine post might give out from swapping it, but it seems like careful installation and matching how the wraps go around have kept this from happening.