Basically the registry key being created via the cd's installer is the only additional thing I can think of because file wise, all the files are in the bundles (Game.exe, Diablo II.exe, .dlls, Patch_D2.mpq, Patch update program, and d2vidtst - I think), the only files that are shared between all of the patches are the core .MPQs.
Normally, people shouldn't be changing files within the Expansion/Classic folders. These folders are just storage locations for files that will be copied over to the D2's root directory when you switch versions. They also store the save for the character files.
Thus, a reinstall for just the files shouldn't be necessary. Btw, if you do reinstall, you don't need to patch. Just install 1.07 from the cd, drop the Expansion/Classic bundle folders into your d2 folder, and you are pretty much ready to go (Make sure that the first version you run is the version in your d2 folder at the time you are running it.. aka 1.07 right after install.. this is so that it is in sync.. aka it creates the LastRanVersion.txt that has the 1.07;true entry stuff).