I just ran into this bug today and am attempting to fix using your method, but I cannot find an option to rename a specific part like that in-game. I can only rename entire vessels.
I solved the problem, or rather found a solution someone else made that worked well.
I used the save file editor posted by Mythos, "KML," found here on the forums:
Once I loaded my quicksave in this editor, it saw the problem automatically and gave a visual warning for it. I was able to double-click the warning, right-click the highlighted attribute, and select the option to fix it. I loaded the save and the problem was indeed fixed. This man deserves a medal.