Something isn't adding up here. If she's getting in 109g protein, that's 436 calories right there. If she's only taking in 662 calories, then her protein would be about 65% of that. Maybe some misinterpretation of what MFP is reading? I can see that they might "recommend" 35% protein for her low calories - a typical normal diet might be 15-20%, and a bariatric weight loss diet might well be 50-60% (or more, at the beginning when we are eating little else other than protein.)
60-80g would be a typical recommendation for a woman with a sleeve, as there is no significant malabsorption involved, though some go higher than that as a means of avoiding "carbs", or under the false assumption that the extra will help avoid loss of muscle mass (it will to the point that one is actually working to build muscle mass, but the only thing the excess does, other than make expensive urine, is to avoid deficiency, but one doesn't need much extra to avoid that - the typical bariatric recommendations will cover it.)
It does sound like a bariatric RD would be a good person to consult, and if she is truly only getting 6-700 calories and still struggling, then there may be some other metabolic issue going on, and some other appropriate specialist may be in order. But a good RD would be a great start in getting a good baseline of what is really happening dietwise. Starting at 400 lb, a sleeve is often somewhat marginal for getting to normal, particularly for a woman of that size (how tall is she - that's a factor as well in determining an appropriate goal and understanding metabolic issues.)
You say that she recently moved cross country - where is she now - that can be a help in finding new specialists. It might be that the VSG is indeed marginal for her needs, and she really needs something stronger. A DS is a straightforward conversion from the VSG (as it uses the sleeve as its basis) and is typically the strongest metabolic tool of the mainstream procedures, so that is also a longer term consideration.