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You need to checkout the file before modifying it -- the first thing a checkout does is replace the local file to match what's in VSS -- and check it in after the changes have been made.
If the checkout step is performed after modifying the file and it is configured to replace writeable files, it will overwrite your changes; otherwise the step will fail due to a writeable file. And normally, checkin on a file that is identical to what's already in VSS will just undo the checkout and not create another revision.
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