If you've got the space, I'd do an extra install for other servers like The Hidden Forest etc as servers adapt certain files that can cause chaos if you're chopping around (Nektulos/Lavastorm here as an example needs to be adapted).
Assuming you go to do that and don't get an option from your Titanium CDs to do another install, copy your original P99 folder to a USB stick (or CD-R or whatever) and then do another Titanium install for Server 2. Sounds like a long way around a big problem but it can save a lot of headaches
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