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[Somebodyelse]

So I just retired my fort to make some animal people adventurers strictly so I could retire them at the fort and make them a part of it. Getting them there went smoothly as I was able to generate them at my old fort having them directly start off as citizens.

Beyond that a LOT of awkward things happened that I'm going to need to break into lists. Some it will probably be known already, but just incase something here is a new issue I feel the need to share.

1. Items
-The first and most annoying thing I noticed was how everything single container (barrel, bin, bag, pot, etc.) had vomited it's contents onto the ground. Over 10k booze all over the floor, dimple dye sitting in piles, mountains of block/bars in stockpiles. This even included a minecart full of magma that one of my dwarves claimed ownership over. RIP jerk that stalled my magma forge construction.
-Although most items were still in stockpiles where I left them, I did see random mounds of items in some far off places.

2. Creatures
-As is already well known, all animals where released from their pastures and all visitors are now hostile.
-Many new animals under my command that lacked the "stray" modifier in their names, most likely an unintended addition by my next note.
-Many MANY merchants listed as being part of my fort in the units screen, all of them could not have their labors managed and seemed to be happy enough to just loiter around acting like residents despite the lack of any control over them. Of note: When I initially retired my fort no merchants were present.
-Both of the adventurers that I generated were indeed full citizens and could be managed like any of my others dwarves. Success on that front at least

3. Terrain (THIS MIGHT BE IMPORTANT TO YOU IF YOU HAVE AN OCEAN FORT)
-Despite the fact all the caves were tightly sealed off with normal walls I had full vision of one of the caverns for some odd reason. Both other caverns were correctly obsured, though.
-The is the one that made playing this out impossible: My embark was on a partial ocean biome and all tunnels on ALL z-levels(even down to tunnels around the magma sea) that were dug out under not just the ocean, but even the beach the waves wash over, were all completely flooded. I'll note this wasn't flooding then entire underground, only the dwarf made tunnels directly in the ocean biome, all other tunnels and the caves were dry to the point of having air next to 7/7 water. My fort at large was unaffected as all tunnels that went under the ocean were deep exploratory tunnels. I'll also note I only hit one aquifer near the surface, grazing it from above to make a well that in no way connects to any of the tunnels below.

That last issue is the real killer and I haven't been able to find any bug reports on it. It's easy enough to reproduce, just embark with ocean biomes on the map and make tunnels in the biome under the ocean in any z-level. Retire fort then reclaim it.

[Shonai_Dweller]

3. Is very annoying and you're not the first person to point it out either.
Get it up on the bugtracker if it's really not there at all.

[PatrikLundell]

The water "walls" are likely another artefact of DF fluid behavior (ignoring the fact the water shouldn't have been there in the first place). If you remove cavern trees standing in water with a ballista, the tree is disintegrated and a hole is left in the water (including the parts were the cap was, if the water was deep enough). A ripple hitting the hole will cause this to collapse, however, so any water filled tunnels should be bricked off, since any disturbance is likely to cause the water to start flowing out. If the tunnels aren't connected to a source, you may intentionally cause them to drain into e.g. a Portable Drain to clear them out instead.

[Somebodyelse]

The water in the tunnel started flowing the moment I unpaused. I'm just trying to say only the ocean biome sections of tunnels were filled with water.

Edit: Found it on the tracker. http://www.bay12games.com/dwarves/mantisbt/view.php?id=5872 Apparently it's fairly old bug that's still in effect.

[Miuramir]

The water in the tunnel started flowing the moment I unpaused. I'm just trying to say only the ocean biome sections of tunnels were filled with water.

I might try this again some time to see if smoothing the tunnels or constructing walls and floors in their place will stop it.

I suspect that this is a side effect of the simplified storage of a worldgen or retired fort; the water isn't stored.  In other words, the game re-generates water when it rebuilds the square to load it (by unretiring and/or visiting as an adventurer), perhaps by something as simple as a check for whether it's an ocean biome + below sea level + empty space. 

I doubt that smoothing would help; however, building doors or floodgates just outside the biome should work to compartmentalize things, and once things have loaded the usual sorts of draining, pumping, and/or water destroying methods should work.