Issues With 1002:

[Angelox]

Are you guys compiling, or are you using the Win32 Binaries posted? If you use the binaries, you only need one folder (c:\eqemu) with the binaries - just overwrite old with new binaries whan they update.

[So_1337]

Binaries. But I don't like a situation (like what was happening), where the server wouldn't work properly after I upgraded. I don't like leaving my players hanging.

Though, if I simply overwrote, I wouldn't have had that issue anyway, so it's a catch 22 =P

[Angelox]

Well this may be your problem - you need have a single "default" directory called "C:\EQEMU" inside C:\EQEMU, you need to have quests, maps, pluggins, etc. but the executables should reside in "C:\EQEMU" (I'm trying to make this as simple as possible for you, so it works and we avoid confusion).
You can always copy the old binaries back if you are un-happy with the new ones. Or better yet, you can make a new directory in C:\EQEMU and call it "backups" (C:\EQEMU\BACKUPS). copy everything in there before you add updates, so you have a working backup.