You want to install on a different drive or partition if you can. If that's not possible, just make a different folder for the new install (you can specify a path when you install). I used to have two Live installs on two different drives on the same computer in order to two box without sharing files.
Also keep your shortcuts to launch the game different - label one p99 clearly if you haven't already done that.
Given that your new install won't have any of the edits required for this server, you should run the patcher and hop on live without issue.
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