Some older workflows may have Alfred 3's directories hard-coded. If they do, they'll still be storing their stuff there, and will break if the "Alfred 3/Workflow Data" directory doesn't exist, so you may have to recreate that folder (or edit the workflows).
Probably a better idea to rename or move the Alfred 3 folder and hold onto it for a week or two to make sure none of your workflows are still using it.
