I did have this working and then made some changes and don't know what has made it no longer work properly:
I have tried using sessions and I have tried just going with simple commands. I have tried with the built in copy script and nothing is letting it proceed to the second and further maps in one bat file. 
I have tried it with the 
"close"/
echo close inbetween each server and I have tried it as it is written below. What is happening now is that the bat is running bottom to top and I only get one server backing up and then the prompt just returns to a new prompt. 
The following is edited removing the identifiers for the servers and host.
Can someone please tell me what I have done that is making it so that only one server backs up and then closes?
    set path=F:\"Testing Bat"
F:
cd %path%
set name1=%date1%"Maps"
set name2=%path%\%date1%" Maps"
set password=<password>
set scriptfile=%temp%\ARK.txt
echo open ftpes://<id>:%password%@<host> -rawsettings ProxyPort=0  >%scriptfile%
echo cd /arksa/ShooterGame/Saved/SavedArks/TheIsland_WP >>%scriptfile%
echo lcd %name2%\TheIsland\SavedArks  >>%scriptfile%
echo get *.(file)  >>%scriptfile%
echo cd /arksa/ShooterGame/Saved/Config/WindowsServer  >>%scriptfile%
echo lcd %name2%\TheIsland\Config  >>%scriptfile%
echo get Game.ini  >>%scriptfile%
echo get GameUserSettings.ini  >>%scriptfile%
echo close  >>%scriptfile%
echo open ftpes://<id>:%password%@<host> -rawsettings ProxyPort=0  >%scriptfile%
echo cd /arksa/ShooterGame/Saved/SavedArks/TheIsland_WP >>%scriptfile%
echo lcd %name2%\TheSecondIsland\SavedArks  >>%scriptfile%
echo get *.(file) >>%scriptfile%
echo cd /arksa/ShooterGame/Saved/Config/WindowsServer  >>%scriptfile%
echo lcd %name2%\TheSecondIsland\Config  >>%scriptfile%
echo get Game.ini  >>%scriptfile%
echo get GameUserSettings.ini  >>%scriptfile%
echo close  >>%scriptfile%
echo exit
mkdir %name2%
cd %name2%
mkdir TheIsland
mkdir TheIsland\Config
 
mkdir %name2%
cd %name2%
mkdir TheSecondIsland
mkdir TheSecondIsland\Config