Hi,
I did run into the same problem few weeks ago .. and didn't managed to solve it.
So if you have a backup or a recent version of your file somewhere (which I hope you have), you better not loose too much time trying to fix the problem, as redoing your scene may take less time.
FYI, I tried to "optimize" the scene, clean the bindPoses on the skeleton, remove all possible unused nodes, export as .ma ... no way.
I also tried to unload all possible plugins (MR, vector ....) and one of them was refusing to unload, saying a file was being used. I use "exotic" plugin to export datas to 3rd party rendering engine, and I assume that was the problem ... but couldn't get my data to save .... I lost three hours, and finally gave up and returned to my most recent version ..
I don't know if your case is similar, but you can try the same cleaning steps and let us know if you succedeed.
Hope it helps,
Guyb.