When I run this process via Matlab will it only run on the protocol open in Brainstorm like other processes or on all three protocols? I assume if I copy the entire protocol into the process one box it will standardise both those tied to subject folders and those tied to epochs in the protocol?
It would be applied to the data files you selected in Process1.
Also will the excess non-used channels in the two subjects folders have affected the ICA/SSP screening for artifacts?
Not if they were marked as bad or as non-EEG.
If you are seeing them when you double-click on the recordings: yes.
If you don't see them: no.