You could create export/import scripts from subset tool for your database. Run the export scripts to extract the data and save this in a secure location. Then drive the publish of the import scripts through TDM so that the same data is always used and not effected by changes in source database.
Another option would be to create a gold copy of the extracted data and store it in a database and for any further publishes you will use this gold copy as the source rather than the actual source database.