The answer is complicated and based on my FLU419. On my FLU, the left and right door hinge pins are different.
Drivers Side Door
On my FLU, the upper hinge has a pin with a head on it, driven in from the lower side of the hinge. The lower hinge pin doesn't have a head on it. In any case, both hinge halves attached to the cab are welded on. Installing new hinge pins must be driven in from the bottom side on the upper hinge and the upper side from the lower hinge if the door is in place. Otherwise, there is no room to drive the pins in.
Passenger Side Door
On my FLU, the upper hinge has a pin without a head on it, different from the drivers side. This is possibly a replacement. The lower hinge pin doesn't have a head on it either. As with the drivers side, the cab side of the hinges are welded on. As with the drivers side, new hinge pins must be driven in from the bottom side on the upper hinge and the upper side from the lower hinge if the door is in place.
I don't know your exact situation. Your original question was where the pins stay when the door is removed. Have you unbolted the door hinges from the door and removed the door? That is what I would recommend because you can then easily drive out both pins completely and replace them with new pins. I would recommend stainless steel pins. Depending on your situation, you may have to cut the lower hinge pin in half to be able to drive it out completely if the door is still in place. Same for the upper hinge with the door in place. We need some more information to comment further. Photos would help.
I had thought, based upon the Unimog I parted out, that the door could lift up and off like a jeep. I took a second look at mine and was not able to get it to remove. I did manage to drop one of the three nuts holding the spring on into my cab frame. So there is that.
All of my pins are pressed into and remain in the portion welded to the cab.
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