I want to report that at least 3 other people mentioned this bug (VST disappearing) on my Private Facebook Reaper user group :
https://www.facebook.com/groups/reaperusergroup/.
Me included, a few weeks ago on Win10, 16 GB RAM and Reaper 5.50.
Plugin Guitar Rig 5 disappeared.
How I solved the problem: I installed 5.40 portable to see if it was version related... Once I added my paths (copy paste the exact same ones as 5.50, of my usual app) and re-scan, it was found on first try. Then I closed 5.40 and open 5.50 and voilà! It suddenly appeared too.
So it looks like installing a fresh portable Reaper changed something in the registry even if it's not supposed... My theory, I can be wrong.
Dali