Agree with many others here who say that muscle loss is inevitable. Catabolism is almost entirely unavoidable on the hike as your nutritional needs demand more of your body than you can provide it. This will reduce your upper body bulk and enhance your lower body. Perhaps the little secret in all of this is that your core will not lose as much as your arms/chest/shoulders. This is because with all that weight perched high up on your back, you require your core to keep your body stable from step to step. It's not the same as doing crunches, scoops or planks but it's constant and "on' all day long.
Protein powder is going to be your friend. There simply is no lighter source that I'm aware of. I would take it on my hikes but after my typical 9-10 day hikes my muscle loss is negligible having first consumed available body fat (going from around 10% down to 6% on average). After a week, I'm right back where I was pre hike in my lifting routine. Hope that helps.
2,000 miler. Still keepin' on keepin' on.
Why is the muscle lost?
If it's being broken down for energy, there's probably not much you can do. It's easy to say "eat more", but everyone tries that, and most people cannot eat enough.
If it wastes away due to lack of use, creatine might help. You probably already know that creatine has been found to minimize muscle wasting in injured patients that cannot use their muscles for weeks or months. It should work for hiking too.
I did mini yoga sessions including pushups and pull ups ( if i could find a good branch or whatnot) each evening. took about 30 mins. great way to conclude a day. I didn't lose much mass, but didn't have much to lose
Friendo,
Devote yourself to your thru hike bar none. I too was going to do pushups and ppull ups and squat thrusts every night but wisdom taught me to relax. Lost 40 or so pounds. Working out almost daily since finishing. Lost lots of body fat. Get jacked after your hike. It won't take but a month or few. I'm looking cut, defined and the best ever. At the very least don't overtrain. Give yourself the extra energy to actually complete the task. Focus.