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The System Shock 2 folder is all you need to play. SS2 does not require any registry settings, apart from the install path, which is only needed to install the patch. Once the game is patched, there is no issue.However, if you move or rename the SS2 folder, you may have to modify your install.cfg to reflect this change.
Just be aware of pontial issues of all the files being Read-Only after you copy them back off the CD