If you have these long requests from a previous client connection that you want to stop / kill, you will either have to manually kill them in:
http://www.mongodb.org/display/DOCS/Viewing+and+Terminating+Current+Operation
Or, when you launch your new client, you can do something more programmatic (get the latest requests from the log, kill them because they are from the previous client). Regardless of whether you can programmatically identify the operations you want to kill and avoid killing others - this is the key here - you may need to add some entries in your application to track your flight.
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