Systems and methods are provided for pre-processing original and new versions of files as part of difference file generation between the original and new file versions, for example byte-level file differencing. Software/executable changes between file versions include primary changes/logical changes, which are defined to be the source code changes, and secondary changes. The secondary changes generally result from the primary changes and are generated by the software compiler/linker utilities. The secondary changes include address changes, pointer target address changes, and changes in address offsets. The pre-processing systems and methods provided use approximation rules between file versions to remove/reduce the secondary changes and encode information relating to the removal of these changes in information of the corresponding difference file.