So I'm running a 5 port hdmi switch with auto switch and my Xbox is run through this to my tv. For some reason when I try to open my Netflix app on the Xbox it shuts down the whole hdmi switch and I lose signal from All sources
Does the switch actually power down? That sounds like a defective switch. Try changing any video settings in the Netflix app.
If it doesn't happen when you connect the Xbox directly to the TV, with the same cable that the switch output is connected to the TV, then it's the switch. You can try turning off CEC in the TV menu.