After editing the configuration file and launching or using the "/itemalchemy reloademc" command the file resets all values to what they were set as before editing. I'm trying to add an external mod and change all the EMC values through the config file rather than one by one in game. Wondering if I'm missing something or if this is unintentional behavior.

I found what was potentially causing the issue and a fix for it. During editing EMC values I changed the order of items to be neater and easier to edit but it seems that was the cause of the file resetting. Editing the values without changing the order then saving seems to have solved my issue, at least on a multiplayer server.