I just had a conversation with Prapper about moving or copying settings files, and using MoveFiles.nsh to do this.
Probably it is better for the launcher to copy them at startup, so if a user would use the PAM backup function while the app is running, the settings would still be backed-up. And move them back at exit!
But I (we) realized Motepad++ Portable moves it's settings out of the settings folder while running.
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You should only run backup when no apps are running. Even if all apps could keep their current data in the data folder while running, if you ran backup while apps were running, you'd miss out on all active data (in memory) and some apps would be backed up as if they crashed at the current point (Firefox, Thunderbird, Sunbird, Songbird, etc).
Sometimes, the impossible can become possible, if you're awesome!