I've had several experiences where I'll rework an area of my factory which causes things to back up. The trains get set to Manual by the mod because no stations are available for it. When stations are re-enabled once things start working again, the trains don't switch back to Automatic mode.

Is there a simple way to fix this? I disable stations instead of setting the train count. Is that the issue? Is there not a way to have the trains check for open stations every few seconds so they can switch back to Automatic mode?

The train station closing condition is also a skip condition, so there will be no problem.

The problem is that the trains are being set to Manual instead of Automatic by the mod. I'd like to disable that behavior or figure out why the mod isn't switching the train back to Automatic once the train has an open and valid destination.

Quite simply, the programmer didn't know you would close the train station.
Me too, but there are more than two train stations, and only one is left open, or there is a depot train station, where the trains can park and wait for it to open again.