Abstract: Method and apparatus for ensuring that file updates scheduled in a Wininit.ini file are applied with regard to previously existing versions and multiple instances of such updates are described. In one aspect, a computer program is installed on a computer system and executed after all file update entries have been made to a Wininit.ini file, but before the computer system is rebooted. If duplicate entries exist in the Wininit.ini file for a single destination file, the computer program determines which entry contains the newest source file based first on the version of the source file, if any, and then on the date/time stamp for the source file. The Wininit.ini entries referring to older source files, as well as the files themselves, are then marked for deletion and/or deleted before the computer system is rebooted.