I once ran out of fuel in my D3 on a long run from Three Ways NT to about 20 km West of Mt Isa. The headwind was steady all the way and all the gear on the roofracks meant I never got the range I expected. I pulled over, emptied a jerry can of diesel into it, and then sat there - repeating this process three times: putting ignition to on for a couple of minutes and then off - to prime the fuel lines.

In all these cases of needing to get air out of the system, there was a case of low fuel, or changing fuel filters. Sitting in a garage for 2 months can't cause that... unless someone syphoned fuel out while it was garaged, or parked there for 2 months on empty... or there was a small leak in the fuel line - allowing air back in over 2 months.

AFAIK, a flat battery can't cause air being pushed into the fuel line - unless one of the above conditions existed. Or something else?