Well, I noticed that they are in a new folder "!workshop" now.
I launched the regular A3 launcher for the first time in a while to install new workshop mods (The only reason I use it)
Ever since then I cant enable them through A3 sync and have to do it through the A3 Launcher.
Also note:
!workshop folder is hidden. When unhidden it did not show up in A3sync.
Inside !workshop are @folders however they look like they are shortcut folders, however lead to nothing except the folder where mod files are installed.