I believe you are correct - the filter was meant to protect the ECM from electromagnetic interference/pulses. Was your repair successful? Were they able to replace the battery while they repaired it? Who repaired it? I believe I may have an M1078A1 with an ECM with a similar damaged power supply.
When I turn on the ignition switch the check engine light blinks for a split second as the voltage meter blips down from 24V. As the check engine light goes off, the voltage meter blips back up to 24v. I plan to disconnect the P2 (front) connector on the ECM to see if there is possibly a short on the engine side in a sensor maybe? I'm hoping to be able to keep the ECM powered on for long enough to establish a connection with a code reader. So far I haven't been able to get a connection.
If I can't get any connection after removing the P2 connector, I am considering using an aftermarket ECM repair service in Fort Worth, TX.