Thanks for the screenshots. OK it's toast, so as has been pointed out three times now you _can_ clean this up yourself (and save the .pio file when done). And personally I'd have just done that from the get go as I'd want custom I/O port labeling to make clear what is what/on what box etc.
The problem description is more like the I/O ports names get screwed up on the very second "stereo pair" "Mic/Line/Inst In / Mic/Line In", as a stereo pair it should be I/O 3 & 4 and that forces all the names of the following pairs to be are wrong, next one can't be 4-5 etc.
Maybe its2loud has seen this behavior? This is not like any problem I've seen before, where that has been more ADAT channel numbers changing as clock rate changes and that confusing things.
First thing you can try is Default the I/O input to Mono and see if the I/O path naming is then less confused. Manually delete (click on the path and hit delete) any paths in use before defaulting the I/O.