I feel your pain stickman393. Just had a similar incident where plugin folders (from several manufacturers) were scattered in arbitrary and hidden folders on my computer and I lost a bunch of presets. HOWEVER, I was able to reopen older projects and then resave the presets again (make a cup of tea...it may take awhile). Not what I wanted to do, but it was cool to revisit the old projects at least and now my preset backup game is a bit more dialed in.
I ended up creating a text document that lists where all the presets (and samples) from the third-party companies are located and now I reference this anytime I need to backup data. But, I'm in total agreement with you that there should be a unifed place where all plugin presets are kept and that this not be a hidden folder. It's easy to see the primary, non-hidden preset folders and assume everything goes there when it doesn't.
And I see your point, gphantom, but in nearly a decade's worth of music production on my personal computer, I have never logged in from a multiple user account. My guess is that the majority of producers also only use one account and this would be a strong indication that the default setting should be more user-specific rather than system-wide, or at least this distinction could be made more clear on install, ie, "Install system-wide if using our plugins on a shared computer", etc.
But the good news is that the presets are recoverable if you have the old projects. Otherwise, you may have to rationalize it as a force of creation coming through to wipe the slate clean so you can start again and explore new settings.
(I've attached a screenshot of my plugin location text document in case it's inspiring.)
-John