It seems like a good idea to create a batch file that regularly checks the current source code from SVN in sourceafe.
You can create a batch file that runs every night using a scheduled task. He will use the sourcesafe command line utility to check the entire codebase on the local file system. He will then do the same using the subversion command line client to get the latest version in the same directory. Then you can perform a check using the sourcesafe command line.
The hard part will detect new files added to subversion and add them to the sourcesafe database. You could supposedly iterate over all the files and see which ones were not checked only after the last check. Another problem would be renaming and deletion handling; I believe that it would not matter that the deleted files remain in sourceafe, as it sounds as if no one is using this codebase.
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