Can you clarify what you mean by the Centlib.prp is getting changed. If you are using a single library for both 2005.3 and 2007.8 flows then the library should be at the 2007.8 version. When you move up through the versions we sometimes add new properties to the flow, this is most likely what is happening, but we only add new properties we do not remove old or customer specific properties and this only happens the first time you open Library Manager . Once you have a 2007.8 library there should be no further changes to the prp file during regular use.
workarround solution in the file CentLib.prp necessary to keep this line for compatibility.
note: my recommandation is to do the migration as soon as is possible.
Nagaraj, you also need to make the file read only to those using the newer version or it will just keep changing it back. So take your original .prp file and make sure it has the *VERSION 15 and then make read only to the ones using 2007 tools.