This would also explain the disappearance of the Plugin Admin itself because of the missing. So all the changes are lost by now, in the case that user didn’t backup those files manually. This way all the files from the above list are missed and therefore NP++ acts like on the first start, creating all of them. After that Plugin Admin starts the NP++ directly, without using the portable launcher. So portable launcher registers the termination of the NP++ itself and removes all the files listed above.

In case of the Plugin Admin update the Admin itself restarts the NP++. But this only happens in the case NP++ would be closed by the user. The maybe changed files are also removed from the NP++ program files directory back to the config directory after NP++ itself terminates and before portable launcher also exits. So portable launcher have to put some setting files from the config directory direct to the NP++ program files directory just before the start of the NP++ binary itself. It looks that somehow it is impossible to make the NP++ portable by just set the right path to the %APPDATA% location. It bases on the art how NP++ made portable and the way the admin restarts the NP++ itself. I think I have a theory, why do we have such issues with a new Plugin Admin. But lucky us, NP++ saves all the saved and unsaved files form the session in the backup directory and doesn’t override them, so the information is still here. I don’t customize the rest of the NP++ settings much, otherwise I would probably see more settings disappear. As somebody here already mentioned, my biggest impact is the loosing of the saved and unsaved files AKA session because the session.xml file get lost. In my case, I also loose some setting in the case of plugins update.

Notepad++ themes 2021