Sir, I only later realized that scrapping factories was probably a bad idea. My guess is that the surfaces still exist somewhere in the game and are taking up "room" or "memory" or whatever. They were empty when I scrapped them. What about them a factory gets destroyed? Where does the surface go?

Is there a way to check which surfaces exist that don't have existing items or entities belonging to them?

If you destroy a factory building entity or item, the interior stays where it is, and the factory building data as well as the surface are still internally managed by Factorissimo for various purposes. Destroying a surface is therefore not something you should attempt. If you wish to reuse these old surface patches you can try the /give-lost-factory-buildings command as per the FAQ.

"/give-lost-factory-buildings command as per the FAQ."

Crap. I read the FAQ, and I didn't remember that bit. Thank you!