Just catching up and admittedly I am the poster-boy on how not to handle what you are facing, but along with that came a good deal of learning the hard way and knowledge I can at the least place in a bag and slide it over to you.
Back in March of 15 this happened, I will even say it was a bit more along as she actually showed signs of remorse and a concerted effort to do what it took to get me back into the circle if you will. Perfect storm as I felt I had learned quite a bit here and felt I did everything right also was hoping that timeline wise she was on the shorter end of the spectrum, the magic bullet protocol was followed to the letter, I did the work but unfortunately I was to close/attached and could not see she hadn't. Long story short she had broke things off with OM for several reasons, finding hair in his shower, knowing he cheated on his wife several times and also cheated on her (I still laugh at that one) and she 'missed her family' ... we went to Retrouville in June of 15, and I felt maybe we had a chance.
Looking back she only could work on herself or the marriage ... not both ... so she chose to work on the marriage and over time it proved to be to much because she never did the work on her, which you have to understand is paramount. No sense aligning the car with a flat tire right? So by November 15 things were sliding back towards a BD like atmosphere, and 2 days after Valentines day I discovered OM clearly back in the picture.. .I confronted, moved out and went NC/Dropped rope.
Bottom line as far as I am reading along in your sitch she feels you pulling away and it very well may be scaring her. I am not so sure one can be scared out of MLC. However you may get her to take some inventory on what things may end up being and at the least maybe she can look within and possibly get some help. You can not ask her to do this which is a tough one ...she has to awaken and see what she has done and attempt to get to the root of why she has behaved this way .... in her case its not one OM its 2, so what is the source for the unhappiness, she needs to arrive there with out any help and sort through her stuff.
This takes time. As much as you want to save the M, there is a time as most here are warning you you have to stand back a bit and let the fallout happen .. she has to hit bottom and so far she has not shown any of those signs ... only fear which is common.