Really, the only files you need to worry about when you patch are anything that ends in .exe or .dll. Although I have plenty of space (so I just back the whole shebang), all you really need to back up are EverQuest.exe (the patcher), EQGame.exe (the game), EQGame.dll (umm... Library for the game), and the DirectX files (dunno remember the names of those offhand though).
If you do that then the only thing you need to worry about is if they totally revamp a zone during a patch. Then you just need to stay away from that zone ingame until the server's updated.
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