Remove Multiline Log Duplicates

I am trying to figure out an approach to a multiline log file problem I have, the device that generates the file does so like a regular running log file however it is FIFO at the point that it reaches 10MB. The only way I can get this file is via FTP and have Splunk monitor the download path, I managed to get all my multiline event breaking working correctly for the most part aside from a few stray events that are truncated from the source but I can live with that. The issue I have is that if I simply overwrite the file with a newly downloaded copy it duplicates many events since the first 256 bytes of the file has a different CRC than before and so does the last 256 bytes of the file. It's really much of the middle portion that is potentially the same .

Is there any tweak or method anyone can suggest to deal with this situation with the goal of not indexing any duplicate events?

First FTP of File Example

MSCi      MSS01                     2010-12-08  09:43:09
40+ random lines
END OF REPORT

MSCi      MSS01                     2010-12-08  09:44:09
40+ random lines
END OF REPORT

MSCi      MSS01                     2010-12-08  09:45:09
40+ random lines
END OF REPORT

MSCi      MSS01                     2010-12-08  09:46:09
40+ random lines
END OF REPORT

MSCi      MSS01                     2010-12-08  09:47:09
40+ random lines
END OF REPORT

Second FTP of File ~1 hour later

MSCi      MSS01                     2010-12-08  10:43:09
40+ random lines
END OF REPORT

MSCi      MSS01                     2010-12-08  09:47:09
40+ random lines
END OF REPORT

MSCi      MSS01                     2010-12-08  09:46:09
40+ random lines
END OF REPORT

MSCi      MSS01                     2010-12-08  09:45:09
40+ random lines
END OF REPORT

MSCi      MSS01                     2010-12-08  09:44:09

Thanks

Jerrad