Since I've stolen away a little time to post, I am adding here a link to the very useful minitutorial by @maxon on fixing elevations of apartment sublots that end up sunken. Because it's great and should be kept easily accessible for others. (But because I have not asked her permission, I am tagging her to let her know I've done so. Maxon, I have no objection if you wish to remove my link for your own reasons.)
Also posting to add a citation and additional usage for the method mentioned in Jo's minitutorial earlier in the thread on stripping lots of sim references.
The citation: for more details about stripping, you may want to check out what Jawusa originally wrote. Jawusa is the one who developed the technique. (I've linked directly there to the post in which Jawusa gives her specific directions, though her overall thread is about the clean, empty templates that Jawusa made using the technique.)
And the additional/alternative usage: you can also strip lots that are already placed in a hood, without ever packaging them again before or after, as long as you know their lot number. However, I have only done this in unplayed lot-testing hoods (the kind I make only to place a few interesting downloaded lots, to see whether I want to keep any---then deleting the whole hood when done, never playing it). So I will err on the side of caution and not recommend that anyone strip a placed lot inside hoods that they care about. Working with a package, especially one you've made a backup of first, is surely always safer! (And if anyone out there knows for sure that my alternative method is also safe to use in actively played hoods, please let us know.)
To find a lot number for any lot in a hood, type in the cheat showlotpackage. It should work in hood view, though it's possible you've got to first use testingcheatsenabled; unfortunately, I can't say for sure because I play with showlotpackage in my userstartupfile. (The whole showlotpackage thing is a tip I got from BoilingOil's own kindly shared userstartup file, in this thread on Leefish.)
Once you've got the cheat running...
Now every lot in every hood displays its lot number when you mouse over it, along with the natural-language (presumably!) lot name you gave it. Just note down the numbers of each lot you want to strip.
From here, the process continues to be a little different because you're stripping that unpackaged lot in place (again, I assume no responsibility if you are trying to do this in a non-throwaway hood). One advantage may be that you can actually put the stripped lot straight in the Lot Bin after; no packaging after the stripping seems ever to be needed, based on a conversation I had with Jawusa about it, much later in that same thread of hers that I've linked.
*Shut the game down and use SimPE to go into Documents, as in Jo's instructions.
*Open the Lots folder you want---it's the one *inside* the Neighborhood folder of the neighborhood that contains the lots you want to strip.
*Find the package numbers you want, and directly open them one by one in SimPE, deleting sim references in all the categories Jo mentioned, plus FamilyTree, as Jawusa mentions. (I agree with gazania in this thread that FamilyTree is really one you don't want to miss---I've only found entries in that category one time, but that lot had a ridiculous number of sim references in all the other areas too *and* was already glitching weirdly when I tested it in a different throwaway hood, so I believe that category of references can be associated with more serious potential problems if not stripped. I had no problems with that lot or my played hood in which I placed it after I stripped it, including that category.)
*Save each stripped package before opening and working on the next.
Now, when you open that test hood, all the lots whose packages you just stripped are clean. So you can *either* package them...or as I said, you can just put them in the Lot Bin at this point. Should be the same and not change the cleanliness of the file either way.
One further note about something I do personally at this point: I just make the actual price of the lot part of the lot name now (so it shows correctly for the package and when in the Lot Bin, like "Tiny Hovel CLEAN20K") rather than re-opening the lot in this throwaway hood again, making a change, then re-saving before packaging or binning. That's because I've seen myself that re-opening and saving re-adds some sim references to the lot, and if it's going to do that, I'd rather it only do it in the final destination hood I want the lot in---so I know they're the right references. But that may be overcautious on my part.
Whew! OK, urge to share knowledge, satisfied. For now, heh.