The offline function sca_removeSharedData() removes folders under /apps
The online function deleteMetadata() removes files under folders.
Inorder to remove the root folders, you can login to MDS schema and in MDS_PATHS find your folder path '/xsd' and delete that entry from that table.
Then refresh your MDS to check whether the folder still available or not.
I hope it should not be there.
It is considered good etiquette to reward answerers with points (as "helpful" - 5 pts - or "correct" - 10pts).