I am having the same issue as you, when my MK3 shuttle goes through re-entry the game will crash. However the time it takes to crash varies, sometimes it’s instant or sometimes it takes until I’m almost through re-entry. I have checked for new updates but I’m to the latest version.
So I found out that none of this crash nonsense happens if you just play on a new world. I have tried a couple of things that I had encountered in my broken save where I cannot re-enter and none of it happens on the new save I made. Some other things that happened in the other world I was playing is where the landing gear sound wouldn’t stop after deploying them and won’t stop even after retracted, and the broken kerbal EVA glitch where you cannot control Kerbals and how they twirl around an axis.