Hmm yes, i did have the same thing on the Wavelab 9.5 update, so i think C9.5 update does need some folders to be copied around. That is why i do not like it is been treated as a new version and a new install. But ok, i know its working ok, just needs some adjustments to get it perfect.
All settings are normally copied over, but it sometimes goes wrong.
If you on windows install some for The User and other stuff for All Users has tripped me up in the past. This upgrade went without any problems.
The only two issues for me were firstly the Lower Zone became reactivated and I had to post here to remember what I did last time - my settings in Preferences had come unstuck. Secondly I had to do a lot of sorting out the listing of plugins - it was a complete mess.
I think that Steinberg might be preparing to get rid of vst 2.4, as many of these plugs were just listed alphabetically and not by vendor or category. I guess I will have to make use of the search function more - admittedly I have more plugins than any rational person needs.
Cubase copies the preferences over from previous versions, but peakae is correct, sometimes it goes wrong.
As for the VSTs, the ones missing install plug-in to a non-scanned position by default - in order to avoid this, one can always make sure to install the plug-ins (the plug-in only, not the contents, if any) to a default path, for example Program Files/Steinberg/VSTPlugins or Program Files/Common Files/VST2.
This way they will always be scanned by a new version (and the collections, if not copied over, can be imported by copiying the Plugin Manager.xml file from the older version’s preferences to the newer version).
For all users should not affect 3rd-party, as it dictates where the content is installed (AppData when ‘For the current user’ and ProgramData when ‘For all users’).