I forgot to mention that I did try both of those, and I do get file errors when I verify it. I tried verifying, opening the game and not doing the bug, then verifying again and I got one file error. Uninstalling reinstalling doesn't seem to help either.
I discovered a weird trick where I can reset the craft design by clicking the new button, which works even after the bug happens. Then if I start my craft with a fuel tank piece then it appears fine and I can attach more modules to it and it seems to work, but any further fuel pieces will get the bug again. If I try radial fuel pieces then bug happens but the other parts of the radial fuel pieces do not vanish, but also cannot be touched.