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I don't know , if I got this correct, but you need to send the modified files and list of deleted files to another machine.
The update/operation on files takes place at 2.00 AM in the morning.Suppose this is script1.
Suppose this operation takes place till 4.00 AM. You can run a script , say script2 which would list the deleted files and the modified files by script1.
Script2 can use find command with atime(or some other) option to find the modified files.These files can be ftp'ied to other machine , say host2.
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