I wonder how they managed to tell trains to stop.

Stop signals. For legacy train control systems, these still work visually and via wires. ETCS (starting with Level 2) does use GSM-R, but everything is fail-safe: No active communication, no movement authority, so the "virtual signal" display in the cab will pretty quickly also show "stop".

Deutsche Bahn trains stop themselves all the time, no need to tell them

Signalling still works, so you can let the trains continue to a safe place like a station and then not let them leave until the radio issue is resolved