The boxes themselves are the game's way of showing that the model file for the "building" model of lot itself is missing. You can be missing props too, but those simply wouldn't display and you would be left with a sparse looking lot.
The best was to approach it, as Tarkus indicated, is to query the lot information in game, and then check the readme of the indicated file to ensure all of its listed dependencies are there. The other quicker, but potentially sloppier trick, is just to redownload the lot and put it back in your plugins folder fresh with all the listed dependencies (sloppy because there may be double instances of things).
Hard drive crashes are a pain in the butt. I've been there before, but you'll get there again. Good luck.
-Matt