You will lose muscle mass (apart from cycling muscles) if this commute replaces going to the gym. That's pretty much inevitable unless you can find the time and energy for weights sessions. When I did about 2/3 that commute my shower was at a gym and I did a mini session (upper/core) most days. You may or may not have that option. If you don't, consider whether with a small investment of money you could get some suitable weights at home. Time-wise the key is to get your weights in while you're sweaty and warmed up anyway.
I chose to have protein bars as recovery snacks after my morning ride /gym session. That might help, but most people don't need extra protein. With that amount of exercise, you can pretty much eat what you like in terms of calories; your dentist (for example) may have other things to say.
If you started fit but not muscly you'll build your legs and the rest won't suffer. What you'll lose is fat.