Unfortunately there isn't a way to "unspawn" a submarine to simulate the sub diving.  What I do when writing missions such as you describe is to give the player a limited time period in which to sink the sub. 

For example, you can spawn the sub then allow the player 5 minutes to find and sink the sub.  After 5 minutes the mission automatically ends.  It isn't the same as having the sub submerge, but it does force the player to act quickly and gives him that one chance you describe before the mission ends.

You can write one debrief for a successful mission where the sub is sunk, one for a failed mission where the sub is not sunk or damaged, and a third for a partially successful mission where the sub is damaged but not sunk.

You can also make sinking the sub a goal and use it to advance the player in a campaign if you want.