I have upgraded from Cubase 8.5 to Cubase 9 using the full (10GB) installer.
PadShop Pro is available as before, for which I have license, however I have no presets available. The preset browser is empty.
Try to reinstall Padshop itself with the library, please.
Could be a roaming data issue.
I notice a previous version of the problem discussed https://www.steinberg.net/forums/viewtopic.php?t=102047
My quest for lost logical editor presets was concluded with help from this video, which may also help you.
Reinstalling using just the PadShop Pro installer (trial download) fixed it. Must be something wrong with the full Cubase installer?
Where VSTs, presets, content is installed feels like a mess. Gone are the days when I felt I had control over where stuff was installed (and understood where it was installed so could fix issues like this) …
As an example, here are some locations for Steinberg content and other support files on Mac:
HD (not user)/Library/Application Support/Steinberg
HD (not user)/Library/Audio/Presets/Steinberg
HD (not user)/Library/Audio/Presets/Steinberg Media Technologies - (e.g. factory presets for Padshop Pro)
HD User (You)/Application Support/Steinberg/
HD User (You)/Library/Audio/Presets/Steinberg Media Technologies - (e.g. user and 3rd party presets for Padshop Pro/Groove Agent)
more user samples and sub-presets, e.g. user and 3rd party samples for Padshop Pro or user wavetables/Macro pages for HALion 6
So it’s quite a mess really, but once you know what is stored where, it gets easier…