So I decided to fly the "Alarm" mission without using the auto start and took a couple of minor GRAD hits whilst taking off. That killed my shkval and gun drive, but for that mission, that's not the end of the world.
Later, however, my main hydro failed, which knocked out my AP channels. Also, when it came to landing, I couldn't extend my gear. I flicked the emergency hydraulics switch next to the gear handle and tried again, but to no avail.
Did I miss something, or was landing very carefully on the shark's belly all I could actually do in the circumstances.
I had a bit of a look in the manual, but found nothing.