Depends what you mean when you say generator is running but A/C units are not. There are circuit breakers on the front of the generator - you didn't mention having to reset them, so I'll assume they didn't trip. Each A/C unit has 120V AC coming through a circuit breaker. You didn't mention resetting either, so I assume that's not why the A/C stopped.
The A/C units also need 12V DC at the thermostat and possibly in other places or they won't run. If your batteries are depleted, when you push the slide, it might drop the voltage enough to force an A/C shutdown.
When running on generator, the Power Converter should provide 12V DC to the thermostats, etc. Might be a Power Converter problem.
Cycle your Auto Level control panel to see how much voltage is getting to the control panel. If on shore power, or on generator, you should see 13.2-13.6 VDC.
It's also possible the transfer switch contactors are dropping, cutting all power to the main circuit breaker panel.
And if your Cyclone has 3 A/C units, and is a recent build, you also have a Precision Control energy management system that could be shutting off your compressors, but the blowers should continue running.
You might want to take a look at our
Electrical System user guide for some pictures, diagrams and more information.