I found the answer.
The reason I was not getting any rows from the cursor was because I was using the line
ContactsContract.CommonDataKinds.Phone.CONTACT_ID
“The id of the row in the Contacts table that this data belongs to.”
Since I was getting the URI from contacts table anyways — this was not needed and the following should have been substituted. The ID was the one corresponding to the contact in the phone table not the raw contact.
ContactsContract.CommonDataKinds.Phone._ID
Exchanging the lines returned the correct results in the query. Everything seems to be working well at the moment.