If you have customised a theme, and have it working just how you like, and you want to replicate the settings on a different install, this is how I would do it..
First of all, install the skin on your second install, so you know it is present
Navigate to the Userdata section of your first Kodi install, from windows you would do this in explorer
\\IP ADDRESS of MediaPlayer\Userdata
From there you need to copy the "settings" file of your theme, this will be found in the guisettings.xml, so take a copy of this file and put it on your local pc
You will then need to open putty and connect to your second install using the ip address of that device, root/openelec are the default user/password for openelec.
Type "systemctl stop kodi" - Your screen will go black! This is normal. If it doesn't, something didn't connect.
Now copy the guisettings.xml from your local pc to the remote location of the second MediaPlayer
\\IP Address of MediaPlayer2\Userdata
Make sure to overwrite the one that is present on the MediaPlayer already
Hop on back to PUTTY and type in the following command "systemctl start kodi"
Your box will now reset. At this time, you'll either be back on your current skin or Confluence. If it's Confluence, change it back to your skin, and see if your old settings are there.
Including the file:
Then when I restarted Kodi it did the usual updating shortcuts but this time all my backed up skin settings and sub menus remained so I was good to go . If you don't restore the skin.shortcuts directory it will always try to rebuild it when you restart Kodi and the restored backup configuration gets overwritten.