Have you tried trash-canning everything in your lot bin in game and then reinstalling?
Nope. And I don't intend to because it would be too much effort to catalogue all the lots I've in the bin, finding the corresponding Sims2Pack files in a huge lot folder and then deleting and reinstalling them. There are also sitting lots in the bin that aren't even packed, just as backups for more difficult building projects. Plus I kinda don't see the point of deleting lots of stuff when I really want to ADD something. Okay, I see, the point being the weirdness that is The Sims.

It is safe to rename the file and remove the extra extension though.
Of course it is safe. I'm not a complete idiot - just not a native speaker and therefore not everything I write is guaranteed to make any sense, lol.
However, it is a lot of work to change the extensions of a lot with lots of CC (sometimes it's the CC that I'm after, not the lot).
So that kinda contradicts your opinion on CC in a lot. Also, I guess you assumed that the lot in question was either something I downloaded or something I had inteded for uploading. Neither was the case. What I tried to do was pack a house with it's inhabitants to get quick clones of the sims. Since that little trick didn't work, I dared to clone the sims (made in CAS, not BS) with SimPe, though it's still the Pets version and I play Seasons. Fortunately that went very well without any complications.
But it still worries me, that I can't get lots back in my game that I packed myself. It's not only the lot with characters in it, but also empty lots.