This is serious stuff and could ultimately leave you with bad credit history if it all goes t*ts up and the company reposses the house.
First thing I would do is talk to the mortgage company fast!!Explain the situation and get their advice as how to proceed - you most definately aren't the only one who will have ever been in this position and they may be able to give you some guidance. Crucially, they may also be able to freeze or reduce the payments until everything is resolved.
After that point, I think getting some legal advice would be a good idea. If your ex has now stopped paying her contribution, you are paying the full amount of a debt which you only own half of, which is not fair. A stiff reminder to her that she can't just walk away from the obligation until the matter is resolved is probably in order.
After that point, as ethel said, your company need to look at whether you can afford this debt on your own. If so, then it may be fine. If not, then you may have no choice to sell where by you and your ex partner will have to consider what they get out costs are on cashing inthe mortgage before the 2 year period is up - sadly, this may eat up any deposit you have put into it.
good luck.