Hmmmm, that's a bit unusual. I wonder if the fact you had the cylinder injection lines disconnected it allowed the system to "vent" ever so slightly over a years time.
I assume your oil injection tank has drained to the point of being virtually empty?
Those check valves in the banjo fitting are pretty effective with fluid (oil) against them, but they're not absolutely perfect.
If some air pressure could leak past the 2 check valves you had disconnected, I could see how the oil might have siphoned out of the oil tank.
I would really not worry too much if that is what happened. Get the engine re-done and hook everything back up, and the oil injection will probably be fine.
Those banjo fittings, with their check valves, would bear watching, but chances are they may be OK.
A curious clue you mentioned was that one cylinder injection line was empty.....air fed backwards toward the pump.....maybe.