Problem with disabled VI's

I have several VEPro7 instances running in my template. Each of them have a bunch of MIDI tracks connected to this instance.
When the VEPro7 instance is disabled, - and the template is saved - I will get this warning the next time I open this project:

Is there a way to avoid this problem?
I want to disable the VEPro7 instance to make the project load faster.