Yes, you can use Data Prep as a tool to handle the possibility that the files used in a reconciliation may change over time. This could, for example, include a counterparty switching to a new file format, or a radical adjustment to an internal file's structure. Using Data Prep essentially removes the need to rebuild your reconciliation process in the eventuality that a file or files do indeed change in format or structure.
Simply create a Data Prep process using the file formats you currently work with. If / when the the file format changes, simply follow the steps listed under What happens if I adjust the Data Prep process? to ensure the configuration has been updated to accommodate the new file type.
Please note that this method of accommodating possible file format changes may incur additional chargeable volumes, due to the data being processed once at the Data Prep level and a second time when volumes are fed through the generic two sided reconciliation.