If you run out of fuel while using the machine, you will get air in the fuel line. Add more fuel to the tank, then prime the fuel lines by pumping the prime button on top of the fuel filter about 10 times or until the pressure increases so you can't depress the button anymore. Then start cranking your engine until it starts (make sure your battery is fully charged). Keep cranking your engine until it finally starts, it will probably take about 10 tries. Try not to run out of fuel to prevent this problem in the future. (BTW I've done the same thing before)I think you're right. The other possible issue is you need to prime the system first, the lift pump at the motor may not be able to self prime?
Bobcat use inline hand primers like you use on a boat, they are cheap yet work very well for priming.