Too much is being deleted when a custom designed ship is obsoleted or deleted. The results is that GC2 will CTD when a saved game needing these files is restarted. The debug file will also have a line that reads similar to
"Debug Message: Can't find ship type FighterG+PMk1 in definitions"
as the last line in the file.
Note: Since upgrading a design doesn't work at this build level (0.77(b).009) I can't tell what the results of an upgrade would be.