Issue running rsync from windows server 2016 to windows server 2016

I may be missing the point but have you considered using Robocopy on Windows. It is similar to RSync however you can't schedule it from the application directly.

This can be overcome by writing a batch file for the copy and then creating a Scheduled Task. Robocopy is free and extremely robust. I often use it to copy files between Linux and Windows using Samba and the network, and the resume capability of Robocopy is really powerful.

As of now (9/7/2017) it is extremely easy to manually add rsync support to the Git for Windows environment without even having to resort to running the Git for Windows SDK.

I stumbled across this post and didn't think it could really be that easy given all the alternatives, but it really is. All you need to do is grab the rsync package from the MSYS2 Package repository and extract the rsync.exe file into C:\Program Files\Git\usr\bin. One and done. It works.

If you need help extracting rsync.exe from the rsync package (which is in tar.xz format), you can either use a compression utility like 7zip or do it directly within the Git for Windows bash environment like so:

cd /c/downloaded_location
tar -xvf rsync.pkg.tar.xz usr/bin/rsync.exe --strip-components=2

This gives you the rsync.exe file in the downloaded location (adjust the package name accordingly). In light of Windows permissions issues I won't try to give specific commands on getting the exe into the C:\Program Files\Git\usr\bin folder. You can copy it via an explorer GUI or via an elevated command line utility (and yes, it will require admin level permissions to copy something into the Program Files folders).

If you want to also use Pageant authentication with rsync over ssh, the ssh-pageant binary is already installed in Git for Windows and all you need to do is add a small bit to your ~/.bashrc or ~/.bash_profile file (see ssh-pageant usage section and Git for Windows wiki). I've modified it specifically for use with the Git for Windows environment and enhanced it with some detection for a missing socket file:

# ssh-pageant allows use of the PuTTY authentication agent (Pageant)
SSH_PAGEANT="$(command -v ssh-pageant)"
if [ -S "$SSH_AUTH_SOCK" ]; then
  PAGEANT_SOCK=$SSH_AUTH_SOCK
else
  PAGEANT_SOCK=${TEMP:-/tmp}/.ssh-pageant-$USERNAME
fi
if [ -x "$SSH_PAGEANT" ]; then
  eval $("$SSH_PAGEANT" -qra "$PAGEANT_SOCK")
fi
unset SSH_PAGEANT
unset PAGEANT_SOCK

I can't speak to how other utilities might or might not work by manually installing them this way, but rsync appears to work just fine. Hopefully that repo will stay and continue to be updated--I'd think so because it's hosted at the official MSYS2 site.