Which mod folder are you talking about? Steam mods are not put into "Documents/Paradox Interactive/Europa Universalis IV/mod" since eu4 version 1.29. Instead steam downloads its mods to steamapps/workshop/content/236850
. Each mod gets a folder which is named after the steam id of the mod. Then the launcher should create a .mod file for each steam mod in "Documents/Paradox Interactive/Europa Universalis IV/mod". The filename starts with ugc_ followed by the steam id of the mod.