When deleting a folder you might get an Error 41 saying it cannot be deleted, this usually means it’s not empty even though it appears to be empty in ProjectWise Explorer.
Please add a folder id column in the view you have (under view -> choose columns…/folder columns -> folder id)
Then it should show the number of the folder that you are having trouble with, in this column.Please go to your server's storage location and check this folder out, you will most likely find at least one file that was left there.
If you do not find any file in the Storage Area, try adding a document in ProjectWise Explorer on the same folder. Revisit the Storage Area and check if you find more orphaned files inside the Storage. Delete them from Storage Area and then delete the document & folder inside ProjectWise Explorer.