The most likely issue is that the new version of Kontakt got installed in a different location than your old version of Kontakt and Cubase is still pointing at the old location.
I assume you can remember/figure out the location where you just installed Kontakt.
In VST Plug-in Manager select Kontakt and under Plug-in Information you can see the path where this old version of Kontakt is installed.
Before proceeding backup both of these locations, just in case. 
Basically you want to merge the contents of these two locations into one location. If it were me I’d put it where NI by default wants to put Kontakt (not the content, just the dll for the plug-in) so I wouldn’t need to think about this in the future. When merging take care to replace old versions with new ones & not the other way.
If you discover that you have any additional paths to NI plugs, now is a good time to consolidate everything in one location.
Then back in Plug-in Manager under VST2 Plug-in Path Settings make sure you only have one path for NI plug-ins and that path is your new consolidated location.