Are you testing on a sandbox account? If so the URL you want to use is https://apisandbox.clover.com:443/..., instead of https://api.clover.com:443/...
Please let me know if this helps.
Getting an empty object is expected and the line item should have been removed from the original order. Can you make sure that you're modifying an open order ("state": "open")? How are you checking if the line item is deleted afterwards?
When I do a get order, the line items are shown even after deleting them
1 Person is following this question.