Program deleting files of exact same size and name

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I'm trying to sync a massive amount of data (roughly 50TB), and I set up a small testbed before confirming such a massive transfer. If the program detects a file of the same name, with, it will delete the file and then resend the other file even though it's the exact same file.  I have ran a program to modify the creation/modified/access dates to be the exact same and it still does it. I don't want to resend 50TB of data. 90% of the files are the same on both ends. How can I get this to stop syncing files are are already exactly the same?


I am also having issues with speed, both connections are 1000/500Mbps. Speed varies between 3-5MB/s  These connections are capable of about 65MB/s upload. 

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