Yes, the Atkins diet with all its protein and dairy and bad fats negatively impacts your entire digestion system, liver, gallbladder, and also your poor kidneys because they have so much of the refuse from protein metabolism to excrete.
The Atkins diet helps people lose weight at first because it poisons the system so much that the body goes "wow we really gotta ramp things up here or this person is going to DIE." But once the body is totally depleted of minerals, it can't deal with it anymore and so ... the weight starts coming back, and you end up losing energy, getting sick, etc.
It doesn't matter what kind of protein it is, altho if I were to do meal replacement with a protein shake I'd trust Metagenics Ultra Meal more than anyone else's, as they use brown rice as their main protein. Or I'd make my own rice milk/egg/lecithin/flax seed oil/cinnamon shake.
Protein overdose is more energizing and ultimately depleting than caffeine or meth. A diabetic with a blood meter knows this is true - they can have Sugar and their blood glucose levels will stabilize quite quickly and easily, but eat red meat and their blood glucose stays sky-high for 4 hours or more.
For good healthy weight loss the only answer is a diet high in veggies, whole grains, no dairy, some fish but mostly legumes and nuts, and some liver management including flushes. That's it. All the rest are fads.