I just found renaming the folder, opening and saving worked for me. I sometimes find these things annoying, then remind myself that UE is open source, if I was that frustrated by anything I could go into the source and change it - then the act of thinking of what I would have to do to fix them makes me feel that the work-arounds are just fine 
Iāve been doing the upgrade āin-placeā. From now on Iāll do it on a copy then just delete the original once Iām happy it converted properly.