The PRC does not affect your NWN installation, and I think the installer simply overwrites older versions of the PRC that may be present, so no worries there.
The way in which the PRC interacts with NWN is by being added to modules. The installer also includes a routine to do this, and here is the one spot where old versons could be a problem. You cannot add the PRC to a molule in which an older version is installed without causing problems. However, depending on how you added the PRC to the module in the first place, the new PRC may function just fine with a module that has an older PRC added to it. If it does not, you might have to add the new PRC to a clean copy of the module. (By default the installer creates a backup, which would be a clean copy of the module.