Since it seems that manually moving or deleting images can cause issues, I might recommend that the program notify the user when it comes across non-existent files as a sanity check. And if the user desires, perhaps Spriter should clean up after itself and eliminate all internal references if the user doesn't care for the missing image(s)?
I ran across this scenario like a couple others on this board, in my case (and I only just started playing with Spriter) I added a mockup image to my project to help me place & align pieces, then I wanted to get rid of the mockup, or at least tag it somehow so my own exporter can deal with it - but no real options to best manage this case (unless I missed something). I manually deleted the image, loaded the project and resaved. The internal reference is still in the scml, which means adding some hackery to my own exporter to get around this...
Perhaps some thought could be given to this, or project management and flexibility in general.
Cheers