Can't you, in Full Reality, give the sub a waypoint and order it to come to periscope or surface, thus getting back into communication to get new orders? If so, one can have the sub going into and out of contact periodically during a scenario...
Yes, that would be the way you could regain control of your sub from time to time. By setting it to come to periscope depth at a particular waypoint, it will re-establish communication with you. However, when you use the Plotted mission like that, the sub is pretty restricted.
For example, it will simply travel from one point to the next and come to periscope depth for its next set of instructions. It will not stray from its plotted path even if it detects something. If that contact comes within range of its weapons, it might fire, but it will not pursuit that contact.
Is it better, then to create an ASW mission and allocate the sub to that?