Can't place items in empty spots, game insists something is there
I downloaded the lot and placed it in a test save. When I went into the lot in build mode, I found nothing wrong so the glitch must have cleared itself by being copied and placed again. I have seen that happen before so wasn't too surprised when I found that I could place things in the spaces you said were glitched. I was able to move things around freely and the only times I couldn't place something was in places you normally can't like in front of a door or a dresser.
So, to get the lot working correctly in your game, I suggest you replace it with the copy you made to post. That should fix those spaces where you can't place things. Keep in mind that you can lose the connection to any personal things like the diploma I saw, the child drawings, garden plants and a host of other things when you replace a lot that has been occupied.
Make sure you empty all the containers - fridge, storage chests, flower station, bookcase, DU chests before you move out. Anything that has anything else in it needs to be emptied and the items placed in one of the inventories. So, before you replace the lot and move out, grab all the personal things and any collectibles including the JA relics, container contents, etc. and dump them in a sim's inventory or the household inventory and move the sims out.
Another way to do it is just to move out and KEEP the furniture. Then when you move back in, you can retrieve what you want from the household inventory and recycle what you don't want to keep. You will keep the connections to everything the sims owned that has one doing it that way. You will still need to empty all the containers and put their contents in one of the inventories though. Also doing it that way has the benefit of keeping the upgrades on everything, and the rocket ship and treehouse fully built. Otherwise, you'll have to upgrade and/or build things again. You'll need to replace the items in the new house with their HH inventory counterpart when you replace a house this way. The other benefit is that you get a ton of bits and pieces from recycling the leftovers. And the HH inventory can get incredibly slow when there's a lot of stuff in it but as you take things out, it does speed back up. And that can take a lot of time, but you'll get a working lot again in the end that's just like it was before the glitch.
Hope this helps.
