Is there some sort of underwater "GPS" tracker they can use to track the sub?
One thing the military does/did to communicate with subs is use low-bandwidth text-only very low frequency radio, but you need colossal transmitters and there's no way the mother ship carries one. Hydrophones are also an option, and IIRC NATO even has a working sound-based modem to transmit digital signals to subs, but not sure if that has spread in the civilian market.
Or fire a torpedo and detonate it.
Probably much lower range vertically.
e.g. every 2 hours, send up a transmitter that sends an "A-OK" on X Khz for at least Y minutes. If you get a bunch at once, or don't get any for a while, or get the "Something wrong" on Y Khz transmitter, you know something's gone awry.