Audiobus problem

I have a bandmate guitarist plug in his guitar into an irigPro interface, while I run cubasis with backing tracks and my keyboards. There is an amp sim app, tonestac, which is put in audiobus as an input, with cubasis the output. Everything is fine until I go from one cubasis project to the next, when audiobus will disconnect the apps and force me to remove and restart it within audiobus for it to work again (meaning to apply the effect). I’m not running any virtual instrument apps, just playing live using my keys, and he is playing his guitar. I’ve noticed the dame behavior using vocalive app when plugging Ina microphone. It’s very annoying for live performance having to remove and restart the audiobus input signal each song. Is this something with IOS9 and cubasis. I emailed audiobus, and they asked me to contact the Steinberg group, hence my post here.

If you are only doing live performance and not recording the audio from the guitar, are you able to set up audiobus with 2 routes, One for the guitar with Tonestack, and anopther for Cubasis and your keyboards.
In fact if you are just using Cubasis for backing tracks, do you need audiobus at all ? Can you not just use the audio you get from the individual apps, as long as they are all set to background audio. Just a thought