This is terrifying, stuck in a small space, probably in darkness, unable to do anything to save yourself. Do they have enough oxygen? Water? What is the bathroom situation like...

Given all of the redundancies they seem to have had for rising to the surface, it seems they didn't pay enough attention to the problem of being tracked and found in case of a problem (reminds of MH370).

I wonder what they could have done?

A comms system with its own separate or backup power system?

A mechanical system that produces a distinct sound on a regular basis?

Mechanical/manual system to release small beacon buoys to the surface that keep accelerometer data and maybe GPS for when it hits the surface so that it's path can be retraced once it's retrieved?

Have a spare sub for rescues?

Have a tracking sub that follows nearby so that at least one is ok in case of an emergency? Maybe it's smaller and remotely controlled?