Were you court ordered away from your children too when she filed the protection order? This may be a legal issue that you receive direction from the courts about.
If not, kids are separate from your situation with your wife. Kids take priority over what you and her are thinking and feeling, they should come first. I hope they are not going to be used as a weapon or bargaining chip.
Stop mind reading, you have no idea what she is thinking and that shouldn't be where your heart is when thinking about your kids.
If you are worried about her taking your visiting the kids as a way to interact with her. That is because you want it to be.
Whether you want to see your kids or not and when you want to is your decision. If or when you see them only make the conversation about when, where, etc. Say thank you and be pleasant. No other conversation about relationship, feelings, etc. Don't rub anything in her face, nothing. Be a dad and focus all your attention on your kids.
Contacting her about your kids does not count as pursuing and does not go against the rules 25 posted. Those rules apply to your interactions with your wife about your relationship.
I know it is scary and any mistake feels like the end. The book says you will make mistakes so learn from them and keep going.
You are reading the book, right?
M:34 XW:34 Together: 10y Living: 9y Married: 7y Son:6 Son:4 Separated: 12/28/13 Piecing: 5/2/14 Separated 2nd: 10/16/14 W filed, but pulled it: 11/5/14 papers served: 1/27/15 D final: 3/6/15