Let me say I'm sorry for your troubles, you're not in an easy situation, and I'm in that boat with you, my 1yr old son's father has been absent since conception. He doesn't even call to see how the child is doing, yet he's sued me to establish paternity and wants full custody.
As for modifying the order you have. You said that he filed to establish paternity. Was it that simple, he didn't ask for anything more? As it stands, you have physical/primary custody, and you have to share joint legal? I thought that just meant that he should be included in the decision making and that you physically hold the child? I could be wrong, I'm currently learning and trying to grasp all this legal jargon myself.
Was there a visitation order set up with that? Or are you expected to share time with the child equally in a half and half situation?
It seems to me, that although to us mother's, the father being absent is serious. We're told it's serious, we read it's serious, but then the court's have a better late than never attitude. It's better to brace yourself for that, so if you do get told that, you won't be so shocked. I have a friend, who's ex was gone for 3 years, he came back, wanted visitation, and her little girl went with the dad out of state for 30 days for his summer visitation, not even a week after the hearing. Shocker, to us yes, to the courts, that's in the best interest of the girl, dad has a right.
It's tough, should you stay doing what you're doing, and wait to see if he does something? Or should you try to modify, knowing he's going to retaliate, and he'll probly get more than you wished in the first place. He could come in and say it's all your fault why he can't deal with you and that's why he's been absent. Custody is such a touchy issue. If you feel he really in his heart doesn't want to be there for the child, and that you can handle what may come out of it, then at least try. But be prepared, for yourself, for whatever outcome may possibly arise.