I can't actually import any files in the trial so I can't say for sure, but I would put my money on you having to re-do the JSON part again with the new layers and such in your PSD.
If that kind of confused you though just go through the process that I mentioned in my reply to your topic and crop the new image layer and save it out as a png file then add to that image folder in your project directory and everything should run smoothly, so you should have two options to go for, whichever you find easier would be the route I would take.
Sorry I couldn't be of more help, I plan on purchasing Spine, just not yet, with Christmas coming up I don't have that kind of money to throw into a new piece of software. However I sincerely hope that my response clears something up for you at the least...
Kind Regards,
Patrick.