I am reasonably certain that in order to make a flute with proper intonation the first necessity is that the hollow of the tube (of whatever substance it may be) must be uniform. Deer leg bones are not uniformly hollow. Virtually any means you might employ to correct this, for instance by drilling or by the insertion of a red hot shaft of proper diameter, will cause the bone to burn. This really smells horrible. Just thought you'd like to know that.

My best guess is that you would have good luck in making such a bone into a recorder type whistle. I have doubts that very many of the ones made by Native Americans, for example, were totally accurate in intonation. That was the beauty of them. Wonderful tones were made by overblowing or underblowing the notes.

I guess what I am trying to say is that if you are determined to make a musically accurate instrument, you have your work cut out for you. If you set aside that requirement, you can have a nice whistle with only a little effort.