Two possibilities here....
1) Since you say it's MyFile.cfg I'll assume it's not .INI or .XML format. In that case, use the InstallShield Text Files Changes view to author a search and replace on the files. The InstallShield custom actions support UAC and Rollback so you'll be good to go there. You will probably need a very simple InstallScript custom action to read the OriginalDatabase property, parse out the part you care about and assign it to another property. Then use that property in the Text Files Changes view.
2) Why have the entires in the .cfg file at all? What application reads these values? Refactor that to not need the cfg files. Windows Installer exposes an API that allows you to query the installer service for information related to installed products. You can ask MSI what the MSI name was for an installed application and then use that information for whatever you need it from. Put the logic in the application and simplify the deployment story for a more robust installer experience.