I don't know which mod is the problem but I suspect this one is. Mine outputting into a chest, a chute then dumps it on the belt. I'm running the autodeconstruct mod, when the ore is gone the mine and the chest are marked for deconstruction. At that point the chute will not empty the chest even if there's space for it to do. I come back to a chest of ore with a chute not emptying it onto the empty belt. Note that the chute doesn't get deconstructed, just the chest.

This is expected behavior. The same thing happens to an inserter once the chest it is drawing from is marked for deconstruction. This is the same behavior that existed in 1.x as well.