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Thanks for your inputs. Surprisingly i tried executing the following command but end up deleting ssh.exe in Cygwin folder when source folder path is incorrect or not reachable. rsync --remove-source-files -v -av -r /cygdrive/c/AmitTest/ ssh username at destinationserver:/cygdrive/e/AMIT/AmitTest/ I am wondering if remove source is doing some tricks there but unable to find root cause why ssh.exe will get deleted with this command. It has happened twice since yesteday and today i noticed this happened when i executed this command. Any idea why this can be happen...

Thanks for info. I was under the assumption that rsync will execute followings steps: 1. Compare first to identify different files (new/updated) --> This is where i am worried due to data size 2. Upload new/updated files 3 Remove source file As per your comment, rsync will compare after uploading to check if files are identical ? Additionally i don't expect to delete directories as i want