I just ran an old version (2.8.8) of Joplin Portable on Windows 10 and it created a JoplinProfile folder in the same folder as itself. I then added the Favorites plugin and added some notes to it. I then Quit Joplin and downloaded the lastest release version (2.9.17), overwriting the existing JoplinPortable.exe. When I started the new version it found the existing JoplinProfile folder and opened with notes and plugins intact.
I've been dropping in the new JoplinPortable exe into the same folder as the original, with version numbers in the name, i.e. JoplinPortable-2.9.17.exe. I just tried it again and it picked up the plugin, but when I upgraded this morning I had to reinstall.
Anyway, I gather expected behaviour is to automatically pick up previously installed plugins, if I can reproduce this again I'll grab logs.