Apparently, when you send an app to the 84+ mode, the app is stored apart from the RAM and ROM backups.
Here is how I noticed it:
I had MirageOS installed and made to work with the MOSPATCH program, which modifies the app itself in order for it to run correctly. Each time I switched to the normal NSpire mode and back again on the 84+, I had to run this program one more time.
Maybe this'll help with hacking the NSpire...