Late Letters of Recommendation

Hi all, wanted to get some feedback on a situation I'm facing.

I applied to Darden and Goizueta in R1, was dinged w/o interview at Darden and accepted to Goizueta. I wanted to apply to a few more schools, so applied to LBS and Sloan in R2.

One of my recommenders (who wrote me a beautiful recommendation in R1) has gone completely off the rails. She answers my texts and in-person visits and promises to write the letters, but won't actually write them. This is a major problem, as I submitted applications to LBS and Sloan under the assumption that she would live up to her word (as she did in R1). I was resigned to the fact that my applications would slip to R3 (because they were missing a rec and therefore incomplete), which sucks but isn't the worst thing in the world.

However, I got dinged from LBS on Wednesday. Quite an unpleasant (really a bit heartbreaking) shock as I didn't think that I was even being considered in R2 because of the incomplete application.

I'm now panicking that the same thing is going to happen for MIT as well and I will have wasted a combined $500 and a lot of time and energy. Can someone more familiar with this process fill me in? I was under the impression that schools wouldn't review an incomplete application. Should I call / email MIT and ask them to consider my application in R3?