Your best bet is to just buy the steam version of sod and use that for all servers sans 1999, but that doesnt solve the different spell files ect from various servers..
You could use the generic mod enabler
http://www.users.on.net/~jscones/sof...cts-jsgme.html
Install this into an eq folder that has been setup for emulator play, then create a mods folder in eq and run this program from there. Now you can create new folders in the mod directory that will hold the various server's custom files for you, ex a 1999 folder, a hidden forrest folder, ect ect. This way when you want to play a different server that has custom spell_us.txt files ect, you dont have to manually move stuff around, or have multiple copies of eq, you just run the mod enabler, select which mod you want active, and it will automatically use the proper files for you (as long as you have a default install and put all the custom files in their respective mod folders)
This doesnt fix your original question about 1999 but would prevent the issue from happening again after you re-install eq...