Could it be that longer chains are heavier and require more energy to move?
Good question, let's analyse it. Yes, longer chains are heavier than shorter chains. Also objects only require energy to accellerate and during accelleration, more energy is required to accellerate something heavy than something light. Once something is up to speed, it requires no energy to keep moving, albeit we have friction robbing the constant speed of it's, well, constancy. So yes, heavier objects require more energy to keep going at a constant speed when cycling because uphills are technically accellerations. In space, once you've accellerated to speed, you stay there with no energy required. We don't cycle in space. It is cold there, and besides, it lacks the whole atmosphere of of cycling.
In reality, a 29-er may require two more chain links than a 26-er. I quickly measured 2 chain links and foud they weigh 16 grams. Therefore, the weight difference (calculated only by the effect provided by a longer chain) is 16 grams. A bicycle and rider weighs....say 80 kilograms if we're kind to the cyclist and his/her bike. 16/80 000 = 0.0002. The weight that you have to accellerate is 0.0002 times more for a 29er than a 26er. Conclusion? The difference is not "massive" as claimed.
However, the OP said, "major loss of energy". Clearly, we are not in the major ballpark. Further, the OP seems to think that the energy losses occur because of the increase in chain length. He/she didn't think this through. The "loss" (no energy is lost, BTW, because energy put into accellerating the heavier chain is returned when coasting) is nowhere near major.
Let's now assume the OP meant something difference - that the longer chain is somehow less efficient, as some posters upstream assumed, which I gauge from their answers, this is blatantly untrue. Efficiency is all about energy losses vs input. A longer chain has exactly the same energy losses in the chain as a shorter chain, if we use the same sprockets for both chains. Energy losses in a chain, as was pointed out upstream, are all about the amount of articulation a chain does around a sprocket. NOTHING ELSE. If a chain is long or short, if it runs over two sprockets of a given size for both scenarios, it loses the same amount of energy.
Energy losses in a chain are a function of sprocket size (the smaller the sprocket, the more arcitulation and therefore the more losses), lubrication and chain tension. More chain tension (harder pedaling) the more the losses. Better lubrication...well that's obvious, isn't it?
So no, heavier chains don't require more energy to move unless you consider 0.0002 significant.