When I updated from the previous version (portable) to 4.8, it cleaned out everything in the app folder, which included my manually installed plugins.
I had a couple of extra dll files that I'd installed in \PortableApps\Notepad++Portable\App\Notepad++\plugins\ alongside the ones it ships with. Is there some other folder that is persistent in the portable version, or this this something that may need to be looked at in the launcher?
Happily, I had a backup of the plugins, so it was easy to reinstall them, and they work fine now that I have done so.
I tested again, and updating 4.8 to 4.8 did the same again, deleting the plugins.