Brunchey is on the right path….
To ensure your send port instance is successful you will want to use delivery notification (http://kentweare.blogspot.com/2007/11/biztalk-delivery-notification.html). You don’t want to mark you file as done if you send port is going through retries due to connectivity or disk issues.
You can use some .Net code to either delete the .flag file or simpley rename it. You will need to write this code in an expression shape or reach out to a .net library to do this work.
You will be able to get the location of the inbound file via the file adapter’s context property in an expression shape i.e
FilePath = MsgIn(FILE.ReceivedFileName)