Small update but with one pretty big bugfix (may introduce other issues if undercover units being in specific groups are important for your mission, but only if this bug appears):
Finally fixed the issue with unresponsive enemies on longer / multi-session missions!
Also, any editor placed unit with "this setVariable ['isSneaky',true]" in its init will automatically be switched to the undercover unit's side and will function as an undercover unit. So you can place an opfor down, set the undercover unit side to west in the setup, and it will all work as it should. This will be helpful for getting the perfect disguise from the start of a mission.
Not that anybody will care, but:
There was a rare, almost mythical bug that I really struggled to reproduce... until yesterday, when no matter what I did, nobody would shoot me (first world problem number 1). Turns out the engine, in all its wisdom, had decided that setCaptive was not good enough, and completely switched my side to civilian. So as far as my enemies / victims were concerned, I was just any other civvie joking around by shooting at them (as a cheeky civilian might). I've now put a check in to make sure the undercover unit's side is exactly as specified in the setup file whenever a change of state occurs. If it isn't, it switches the unit to the correct side. The downside of this is that we have to create a new group and delete the old one, so group-specific coding will get lost if this engine bug appears. I can't see a way around this though until the original engine bug is fixed, which is unlikely as I have no idea how to reproduce it. So it's a workaround / hack, but should do the job. And the script should be pretty much bombproof now.