The file will be deleted from your Box account. The folder will be deleted from your Box account. When deleting content from your local Box Sync folder, Scenarios where you will not receive a 'Confirm Deletion' prompt: You will no longer see this pop-up for any future deletions of folders that you own that contains collaborators.
You can optionally check the Always delete check box if you always want Box Sync to delete the folder on your Box account.