During the final battle, I looted all the scavengers inside the ship, then went back on deck and took the dinghy down. Since I was encumbered, I stored all the loot in the big box on the dinghy, and then went to loot the scavengers on the ground. Captain then tells me to fire up the switch, so I do, and ... well, it was rude, but I laughed.

Anyways, I waltzed over to their new location, and searched all over for the dinghy which would take me up - needs a very long rope, of course, so of course it wouldn't go down that far. I entered the building, took the elevator up, got all the stuff, then went to the dinghy. To my horror, it wasn't there - it must have fallen off somewhere along the journey. Does anyone know if the dinghy fell anywhere so I can walk there and get my loot, or does it just... disappear? In which case I need to load an older save...

I couldn't find the dinghy, and so I reloaded an older save. This time I was smart - I put everything into the first-box on the barrels beside the terminal on the way to the dinghy. Looted the scavengers on the ground, then flipped the switch. Watching closely, I think I saw the dinghy fall off when it hit the building, but searching the ground around the building yielded no dinghy. I was smug and happy, though, as my stuff wasn't in the dinghy, and merrily waltzed off to sell the loot from the dead scavengers on the ground, then got sidetracked and did a bit of other stuff, then came back to the USS Constitution to pick up my loot in the first-aid box.

Nothing... just a Stimpack and Rad-X

It seems that it's not the same exterior cell, so the contents are replicated, not moved. Either that or it respawned, but surely it wouldn't respawn in 2 days?

Time to reload again...

My guess is that this is a scripted reset. It is obviously a story/game-changer when the ship moves.

As you pointed out, it is likely changing cells too.

Just seems like they would have to do a hard reset on it, to be able to reuse it in another cell.

This would clean up all the garbage (visible in game, and/or code level) left from the previous cell/mission.

I would just go home and dump your stuff and come back. But I use fast travel, you might not.

Edit: typo

Sorry, but this made me chuckle. Okay, laughed out loud. Go home, dump your stuff, then have your adventure.