Not sure if this problem was solved or not, but also similar situation happened few times to me (Retrologue/Padshop presets not visible and not usable even when the plugins were removed and reinstalled) and the solution was like this (works for both Retrologue and Padshop):
Go to the presets browser in the Retrologue instance and expand the location tree view. The chances are that instead of “ticks” you’ll see small red squares there which mean the cubase cannot read the directory tree on your PC for some reason. Just “re-tick” them which resets and rescans directory structure. This can take a few seconds. Also switch on the “include folders and subfolders” toggle.
Correct look (presets visible and selectable) should look like at the screenshot below. Marked parts are those to be checked.
Well, I think I found a solution for this. Had also the problem that after setting up a new desktop witch Cubase Pro 11 that my Retrologue and Padshop Presets were missing. It seems like there has been a change in the Steinberg routines and these two specific plugins need to be registered in the Library Manager.
So, what worked for me:
Install Cubase and all the plugins including Retrologue and Padshop
Go to the Cubase Download page and look for the “Content” files for Retrologue and Padshop
These are .iso files, so mount them and doubleclick the included files. Library manager should open and ask for registering the content.
There you go, next start of Cubase had all presets included
Hope that helps anyone who still faces this issue.
