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Excluding Database Files from DFSR - 2012 Server

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Two Servers that Replicate from one Site to Another. Due to a Program (Clipmate) a database File DFSR is been stop from replication or Replication isn't working at 100%. Also is it possible to Stop Index.bat files from been replicated? It also causing DFSR to slow down. 

Both Server are 2012 64 bit. I would like to stop the files from been replicate since it causing some File Violation. I would like to know if this will affect anything? Would i need to reboot the server to clear File Violation? Do i need to restart any services? How long it will take? 

Thanks for all the information!


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