Ah. That is odd. You're the first person to ever report such an issue. It's especially strange this is only effecting the original art folder.
It will be very hard to fix this if we can't reproduce it and figure out what is causing this specifically for you and not other Mac Spriter users... hopefully we can figure the cause.
In the mean-time, I think it would be easier for you to use a search and replace function in a text editor to simply modify your new character map to be pointing from the images int he original folder. You can load an scml file into any good text editor to manually edit it.
I'll see if I can replace this character map setting bug on my mac and report back here.
