Hi Jared,
In the EEG hyperscanning setup I could see previously, the recordings of the two subjects were saved simultaneously through the same amplifier in the same file, and therefore the coherence analysis at the sensor level was not more complicated that with a single subject.
If you have multiple files, this would require some more thinking but I would not expect any major problem. The main question is how to organize the files in the database. After that, the connectivity measures you would use between sensors or ROIs would be the same across or within a subject, wouldn't they?
Francois