After a long period of error messages in Nuendo, I've finally solved another problem which has cause me tons of head aches.
Apparently the mixer view (F3) in Nuendo/Cubase does not show all Inserts for the channels in the Mixer. By hitting the "Show all Inserts !" a few old plug-ins no longer used, would show themselves. These have now been removed, and my project template is again healthy albeit not optimal yet. This is something I will address in the future, but for now I just want to record:D