I can’t find the source of problem, but MIDI IN 2 is always recreated for me, even can’t find any MIDI track / layer, that is routed from “MIDI IN 2” port. Deleting, closing, opening VSTLive, opening the project and “MIDI IN 2” is inserted to last port again. Maybe is better to use booth MIDI IN 1 & 2 as spalsh screen also involves them?
That’s a bug I encountered a while ago as well. At a certain moment midi inputs were created every time I opened VL. Up to 10 inputs and then nothing worked anymore. Now it is stable for me, only when I start VL without one of my midi USB devices plugged in, there is a risk something goes wrong again.
Hi @TobiasV , for me only “MIDI IN 2” is recreated once if not found under Connections. So I guess, I’m lucky compared to your 10 inputs 
MIDI IN 1 and MIDI IN 2 are default ports. They will always be recreated when you start VST Live, and are even forced to the first availabe device bus if you set it to “(nc)”. This is intented, otherwise for first time users, or after swiping clean etc, there would be no sound. You may rename the default Ports, but if you do, you have to set (at least) your default Layer Input to the new name, and save it using “Layers/Save default Layer” so to prevent continuous warnings when creating a new Layer, Part, or Song. When you save a project, it will save Port names and associations and restore those when you load the project, regardless of default port settings.
Different issue, or solved.
Thank you for your answer! I think then it’s better to keep these 2 app default input ports as they are, and creating my additional ones on the top of them. (They won’t bother me there)