A .lua file is not just a data file. It can actually contain code in the LUA programming language (see http://www.lua.org/). You could modify the users.lua file to programmatically get the updated users list from your own database. You can then manage that database using your own application. Alternatively, if you want to use the EMS API to send commands to manage your database, you could use the LaunchProcess API command to run your own scripts to manage the database.
Please refer to the API Definition Guide for details on the LaunchProcess API command: