The hard drive search was a good idea, which frankly I should have thought of before. I just found that it had created a \Beyond the Sword\Assets folder on my desktop, containing CvGameCoreDLL.dll, .exp, .lib, and .pbd, all dated to 4:04 pm yesterday. I'd looked on my desktop before, but I guess I didn't look closely enough at the first column, where I guess it went because I'd recently deleted some stuff. It also found 2 DLLs in modcomps I'd recently downloaded and was thinking of merging with my modmod, but having the mod name in their folder name made it clear that they are not what I wanted. A file size of 6.64 MB looks about right too.
I started a game, and it is working just fine so far. Well, mostly fine, but I do need to go back and add the graphics for the UnitStats button and the Armageddon counter, as well as a lot of textkeys. The .ini files probably need to go back too.