ThornkinUnfortunately, I think all you'll get in response to this are anecdotes.
I had generic blank PBT XDA caps from YMDK on original Box Jades for a couple of months and removed them all with no ill effects (no apparent cracked stems, no extremely loose stems), but when I installed those caps on a board with Cherry reds, they were noticeably loose (though still none so loose as to fall off). So my personal experience is that, while the caps were not damaged, they were certainly altered.
I bought new Box Jades anticipating Canvas -- I don't want to loosen an expensive set. Since I'm only covering a Planck, the switches were only another $17 from NovelKeys.