Yeah, update would overwrite those.
But I notified the developer of fapman to change the background-behaviour so it would take the actual desktop-image instead of theme's image. Maybe he will change that in future update
And about that file-dialog to use own images; it's doable quite easily, but then again the user's image should be in right format (png) and sized properly already to be fully functional. I have no idea what would happen if user tries to set image which has wrong dimensions etc. So propably I'll leave the "heavy" customizing for power users who will do it manually.
Yeah, propably the maenotify does some caching it's own, dunno. But what do you need the maenotify for with PR1.2? I though maenotify only adds notifications to lockscreen which now comes with PR1.2 automaticly? Or does it do something else usefull also?