I conquered an Orichalcum Mine. It started harvesting.
When I left with one of my to Manticores, it stopped harvesting.
Had to leave with all aircraft, to return and restart harvesting.
The same for the Quarry.
Normally one aircraft should be enough as long as it has at least one soldier on board. Are all of your aircrafts manned with soldiers? I’m not sure if only a vehicle also work 
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All aircraft were manned. When I returned with the exact same aircraft, the harvesting began.