That is correct. And that is in fact the way it works with all EQEmu servers. Every one is different. The changes put in on one server will not be compatible with the other. This is why they tell you to back any file you change up before copying over changed files at server set up (and the patcher should do it for you).
It's preferable for you to just have two installs. One for P99, the other for another server of your choice. For example my Titanium install is for P99, my Underfoot install is for PEQ.
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