Good question, I can understand how you would expect it to behave in that way.
Our API works slightly differently in that you have to pass the phone number ID as well as a "_deleted" JSON property set to true. The phone number ID can be found in the response of a GET request to the party endpoint.
For example, to delete a number with ID 23406 and add a new number 123456789 your request body would look like:
Update operations for addresses, websites, email addresses, tags and fields also work in the same way
Does that make sense? Let me know if you run into any problems or require further clarification.