Yes, it works the same way that adaptive spell damage did. The Added Melee Damage from Titan’s Femur gets added to the skill in whatever ratio of base damage that skill has. When you convert the base damage of Upheaval to cold, the damage becomes cold damage.
Note: you can still have elemental typed prefixes, so Added Melee Physical Damage prefix still adds physical damage as before. But you can also still get Added Melee Cold Damage prefix if you want it all to be cold.