Thanks @JulianOes for your reply! I looked more info the Mavlink failure injection, and the best seems to be to disable receiving Mavlink message on the drone (so the telemetry is still being sent to the GCS).
I also noticed (as mentioned in this post) that failures in gyro and accel result in jMavSim freeze. Since these are not tested in the CI, I can’t really say when this error was introduced.
The code in PX4-Autopilot/src/modules/simulation/simulator_mavlink/SimulatorMavlink.cpp at 710286da722beae72a488af52b6c1e603f68eea7 · PX4/PX4-Autopilot · GitHub seems to be pretty straightforward, so it is not clear to me what causes this freeze. Any suggestions as to where to look? Or is the failure injection generally deprecated / rarely used?