If you're happy with the behavior of the portable install of REAPER now that you have changed the plugin scanning preference in that install, you could just leave it that way. You can always run a plugin scan on demand later if you need to.
The right-click menu you are referring to is called the "jump list" and that is managed by Windows, not by REAPER. If the jump list has been cleared, it's probably because some cache has been cleared by Windows, or because the shortcut itself changed in some way (maybe REAPER was updated?). But that's a Windows thing, not a REAPER thing.
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