The code in the question looks like it should work. Double check that a FriendList entity which matches the select statement actually exists in the datastore.
Some suggestions:
deleteContact = db.GqlQuery("SELECT __key__ FROM FriendList WHERE myNum = :1 AND friendNum = :2", myId,friendId)
result = deleteContact.get()
if result is not None:
db.delete(result)
else:
logging.error('result was None')
Since you aren't doing anything else with the results, only retrieving the keys from the datastore will be more efficient. Not a big deal here since you're only getting 1 result, but it's something to be aware of if you later need to delete a large number of entities from the datastore.
Since you only need one record, calling deleteContact.get() will only retrieve one, but it will return None if there were no matching entities. db.delete() will throw BadArgumentError if you pass it None, so make sure to test for it.
Alternatively, deleteContact.fetch(1) will return an empty list if there are no matching entities, which is fine to pass to db.delete(). But if you want to ensure that an entity was actually found you would need to make sure the list you got from fetch() did not have a length of 0.