FWIW, TWoTS has a mission (LAB) like this. Looking at the ruleset, the first stage has startingCondition: STR_SURFACE and the second has:
startingCondition: STR_UNDERWATER
shade: 0
depth: [0, 0] #Because startingconditions dont work.
Not sure how well this works though. I don't think the engine is designed to work like this, and you can continue using land-based weapons (at least stun grenades) in the second stage (and I doubt the underwater-only equipment that you didn't get in the first stage will appear on the second stage).