Can't be of too much help. My guess is either damaged rings or carbon residue from oil seeping past rings while on side.
I have a Kubota 3 cylinder tractor and stalling it in normal circumstances should not cause a problem. On its side, maybe fuel starvation if the tank is gravity feed to injector...oil starvation to the crank and sieze...sump oil filling the underside of the cylinder making piston cycling difficult, eventually stopping the engine.
Crud I would think is sump oil having leaked past the rings.
Did you use CRC or such to get it started again? Or did it start of its own accord on the starter? Ether shouldn't be used on diesel engines unless manufacturer specifies its use - otherwise you risk damaging the rings from premature ignition (my understanding).
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