Ideas
The first issue I had for a long time was the game resetting certain lots to a previous lot type, so e.g. a residential lot suddenly was a gym again and had a family live in it. It was easily resolved by selling the lot in manage worlds and then going in via build mode to revert it back to residential.
Then about a month ago I put two R-rentals in the same neighborhood. What happened for the first time there is that when I went into live mode in any of the lots in this neighborhood, it showed the other lots - exept for the one I was playing at - as either empty or a previous build I had there before. When I went into manage worlds or loaded a lot either in build or live mode it was still the correct lot. I resolved the issue by reverting one of the R-rentals back to a regular Residential.
Aaand recently this same thing happened in two other neighborhoods and some lots got deleted altogether.
I have a lot of R-rentals, almost got up to the 99-per-save limit.
I use quite a lot of script mods and some cc.
I tried a factory reset and am currently putting the game back together. Will update this post as soon as I'm finished.