I lost sims and lots a while back, I wouldn't move them between hoods but they had disappeared. I'd seen at TSR someone explain how to do this, they said their sims and lots went after installing an EP. I found it worked for me when I needed it, if you want to try it might help you.
Keep in mind that
because you've moved occupied lots to the lot bin you've already duplicated the characters, and those extra's might have similar character file numbers (I don't know if they'd appear as a family though), or complicate things in some other way.
I do know it will mess up your hood eventually, so it will be a short term fix if it works. I don't know if it's 'awsome', approved of, or where the original information came from. It fixed my issue when trying to work something out in a testing game but I didn't play it longterm, it would be good to know if anyone thinks it's a bad thing though, I don't want to recommend anyone doing it again if it's potentially dangerous!
To make the family appear in your game, open the neighborhood in SimPE (Family Information on resource tree/name of the family) and change lot instance to "0x00000000" then commit/save as normal. This places the family in the sim bin. You'll probably have to adjust their funds to get the house back, I think mine were reset to the 20,000 they would have originally had.
The lots are saved in the Lots folder inside the particular neighborhood folder. You have to go through the lots with Clean Installer and move the ones you know are 'lost' to a empty 'working' folder. The original lot will be called, for example, N001_Lot61.package, you need to change the name of each lot to "cx_
xxxxxxxx.package" where the red x's are numbers.
For mine, I removed the original main My Docs/EA Games/LotCatalog because mine was quite full already, that made the process easier. It didn't matter which numbers they were because when they're placed that changes their name again, so it didn't affect any similarly numbered lots in the 'real' LotCatalog folder which I replaced when I'd finished.
But if you don't want to do that, make a note of the last number you have in that main LotCatalog folder, for instance my last one currently is
cx_00000193.package , so the new ones would be renmaed starting from cx_0000019
4.package onwards.
Once they are renamed, if you've moved you original LotCatalog somewhere while you do this, put them into a new folder called LotCatalog in My Docs/EA Games.
If you've taken into account the files that you already had in the original LotCatalog, just put them into that folder.
They'll then be in the lot bin, ready to place and move the families back into.
I'd say it happened because you shut the game down before it had saved the changes you made to the neighborhood, rather than because of any bug...