Found the answer myself and here it is should anybody else need it.
from hoggit
Basically, you don't need to install Liberation on the server, but you still need to create the same folder structure. So if you have it in "D:\Games\Liberation RC10\" then create the same directory on the server too. Then the system should generate the file in that empty folder.
From Khopa:
"So, if you want to run the mission on another computer (such as a dedicated server), you should have the same file structure so that a dcs liberation folder exists. It's kind of hacky to do right now. And on this other computer the manipulation with the MissionScripting.lua file has to be done manually as well. I don't know if you are aware of this."