I also had some issues switching from Komplete 10 to Komplete 10 Ultimate.
From what I recall I ended up uninstalling all of Komplete 10 then reinstalling Ultimate.
I probably could've tried to resolve the various issues individually but it seemed to be the least painful solution going forward. Granted you've got to install all that material again but the other issues (upgrading K10 plugin errors, etc.) evaporated and you're not going to get a surprise down the line when a new update appears.
Aside from this the only issue I had with the Service Center was the old K3 plugins FM7, B42, etc staying activated.
In general I've found the best way to avoid or at least minimize issues with any VST installer is to
- Excluding VST3s - never assume that any installer system knows where your VST plugins are located.
- If possible specify separate locations for 32 and 64 plugins versions.
Some companies use the same file name for both,
some installers will have problems or lock up if you specify the same folder for both. - Disable options to 'Delete files after successful install'
Installers sometimes don't correctly interpret installation failures or you may need to reinstall at some point.
Best regards,
...Steven