you are best off grabbing Advfort and use it for building a bed, so that you can sleep with out unloading the world.
since the new update for it allows you to 'rest' which bypass the need to jump to the travel menu and unload everything.
also if you get hungry and can't feed yourself you can always build a chair to 'eat' food though I never tested the eating job to Advfort.
okay I just tested this out but yeah units will stay in cages on a random chance, like there's a random chance the unit will break free from their cage or the game straight up won't remember them being on the site
caged wild animals will not stay in build cages and tame ones will pop out of their cage and wander around the site edge.
Ah bugger. This bodes ill. There has always been an issue of the game not respecting positions of creatures if you reclaim.
From what I can tell, when you offload a site, DF converts all the data into lists, and then does some handwavy stuff about where there should be.
From what you are saying it sounds like that this is still going on to a slightly different extent. I think un-retired forts still respect caged vs free.
I may resort to adv fort as a last resort.
As a side note - I'm half of the way there, and I'm in red sleep deprivation. My dwarf has been trucking away, and I've been keeping a journal for this entire endeavor.
Some of the funnier moments were
"I wonder what the animals think, seeing a dwarf barelling down an empty road on a minecart, with a dragon in a cage attached. Run, I assume. "
It would be a pain to upload the whole story though, its been written in a word doc.