Hi, I'm Heather, an attorney with 15 years experience and I'd like to assist you for informational purposes. From what you have stated, it sounds like you obtained a custody order against your boyfriend, which awards you custody, but now you have reconciled, and you are wondering what to do with the custody order. If I have misunderstood the situation please let me know.
If you have the custody order, I would just keep it in place, in spite of the reconcilation. If you live with him, you are still exercising custody of your children. And in the unfortunate event that you do split up with him in the future, you will already have a custody order in place.
If you actually do want to remove the custody order, then you would need to file a petition to modify your custody case, and state that you and he have reconciled and are exercising equal custody. That would be the most expensive option, and it would not protect you in the event of another split-up.
I hope that has been helpful.