Assuming this is happening during normal operation, and not at the time the alternators are switching just after startup:
The Rotax EMS will only detect an alternator 1 (A) failure. Alternator 2 (B) is normally connected to the airframe and is not monitored by the EMS. The indication that alternator 2 (B) has failed would be an amp meter in the negative range and declining battery voltage. If configured in the G3X, you may also get a Crew Alert System (CAS) message as you describe.
If alternator 1 (A) fails, the EMS will take alternator 2 (B) and you will get a warning via the lane warning lights. You will at that time see a declining voltage and negative amp reading on the airframe power bus, and possibly a CAS message if configured and the parameters are met. So it’s possible that your EMS is sensing a problem with alternator 1, and taking alternator 2, but you did not mention a lane warning light so that’s unlikely.
In the absence of a lane warning light or master warning light, I believe the “Alternator Fail” message is coming from the Garmin Crew Alert System (CAS), independent of the Rotax EMS. This is set up in the Garmin configuration mode and typically is set to come on when the airframe voltage drops below (or goes above) a certain set point. This is validated by the fact that turning on your backup alternator solves the problem (restores system voltage). You can look at the configuration of this alert to see what voltage it comes on, but I suspect you may have a problem with the Rotax internal alternator 2 (B) system and it’s not keeping up with your airframe loads. This could be a regulator problem, a wiring problem, or the stator itself. You could start with downloading the G3X logs and looking for CAS messages and the aircraft bus voltage these occurred at. You can also look at the BUDS logs and fault history, but if alternator 2 (B) is failing that won’t throw a fault since that voltage is not being monitored by the EMS during normal operation.
It is important that you investigate this because alternator 2 (B) is your engine electrical power backup. If the alternator 2 (B) system is failing you won’t have a reliable automatic failover if Alternator 1 (A) fails. In this case the engine would stop and you would need to use your Emergency Power Switch and restart the engine. You could then tie in your backup alternator, but this all requires pilot action.
