I have come across this so many times and it has spoiled my playtime in ksp2
What happens is when reverting to VAB sometimes your ship separates itself into separate parts and spawns under the VAB, but now you may think "oh then just bring the pieces up and put it back together", You can't, The pieces lose their connection points and you can't put it back together so I just have had to rebuild my ship. Another thing is when you zoom in too close to the ship while it is under the VAB it completely leaves the VAB entirely and your camera gets stuck. One last thing is that this can also sometimes happen when just loading a ship in the VAB.
All in all I am happy to be a part of the process to make ksp2 as good as its predecessor.