Hi Geez, thanks for the response.

I'm not sure what changed, but I restarted my workbench and my mod files have reappeared. Although, they are still locked as read-only.

Where can I find "Pack Project"? Sorry, I'm somewhat new to this.

Actually, I just noticed another one of my mods is completely gone from the directory. It seems to happen after I hit publish.

Pack Project == "Publish to Workshop" in Resource Manager

I was linking my mods manually by loading the -addonsDir in steam for testing and I think that when the game would update a mod, it would wipe the old one from the addons directory, if it was in there.

addonsDir adds mods to addon list. If you are using folder, where mods downloaded from workshop are loaded then it is basically telling engine to read data from there, instead from his project folder. You should stop using addonsDir and use https://community.bistudio.com/wiki/Arma_Reforger:Mod_Project_Setup#Adding_Other_Existing_Projects this instead and make sure that read only version of is not listed in Enfusion Workbench Launcher