First, if you have had this schedule and the children have remained with you in your home for the last three years of overnight then you have primary physical custody. If she were taking the children to her home at night this would be a different scenario.
(As a side note, I would not want my ex being in my home for any reason because I would never feel free to move on with my life…this is just my opinion, but you should probably change this arrangement and file for divorce.)
Second, she can NOT take the children away from you. Unless custody has been decided by agreement or court order, each parent has full access to custody. If you do not have a separation agreement for custody and support along with ED, I suggest you getting in to an attorney.
Last, if she is threatening to take you to court over everything, maybe you should consider calling her bluff. Consult an attorney. But I will tell you the first thing he/she will tell you is to get an agreement signed, change the locks and do not let her back into your home. If she has a home, she should be looking after the children there. Child support is based on the number of overnights the children spend with each parent, based on the scenario you described, you would be entitled to child support from her. You may be able to settle for less that the NC guidelines amount since she does watch the children during the day and she may be entitled to alimony, but still you should see what your options are…
Bottom line is, this situation has been going on for 3 years and if you want it to change, you will have to change it. If you truly do not want your marriage to work, you have been separated long enough to file for divorce. But be prepared…if you have let this happen for this long, it’s likely to get ugly when you attempt to change things. She will tell you you can’t do this or can’t do that…research on here. Know your rights. She may tell you that she will take you to court. Get to an attorney so that it’s in writing. There are things you can do to keep her from leaving with the children and moving away. She may threaten a lot of things but looking at the big picture, it looks as though she is still very dependent on you. Hang in there and maybe some of these other folks have some input.