Hello,
I am not entirely sure whether I understand your question correctly.
I assume you have several MIDI-Tracks in Cubasis that trigger other background apps via Virtual MIDI? So if these apps do not support Audiobus, there is no way to get the Audio from these tracks into Cubasis. Thus, an Audio Mixdown results in no Audio.
Or do these apps support Audiobus and you get no Audio when doing a Mixdown? So please provide us with some more detail that we can help you.
Kind regards,
Frieder