Child custody

My wife and i separated two years ago. I found out that she had an affair with her officemate. To make the long story short, i wanted to raise our children as even before her infidelity, her dedication and attention to the children was always an issue. I couldnt understand why she didnt show the level of importance a regular parent would.
As such i consulted a lawyer on how i could have custody of the children to assure myself somehow that i can decide on all things or matters involving the children without her, among other things.
My lawyer came up with a post-nup agreement that we both signed peacefully and willingly.
Question: If the kids (Boy 8yo and Girl 6yo) turns out not to be mine, will i loose custody?
I love my children and they are my life. Even if they are not of my blood, they are my children no matter what. I am afraid that i may loose them legally if they are not actually mine.

In a marriage the husband is counted as the father automaticly.
To change that it's normaly the FATHER, who question it in court.
To prove who is NOT father are blood tests enough SOMETIMES. (=Not possible blood groups.)
To prove who IS father, DNA tests are needed and they are expensive.

I don't know what happen if the MOTHER go to court and winn to get the husband to NOT be counted as the father, but I would be very SUPRISED if the mother ever do, because:
1. By that the mother would ADMIT herself GUILTY to adultery, which would be a CRIME, which I believe can be punished with jail.
2. If the mother winn the p1 case in court, then the FATHER can use that to demand compensation for the support he has paid during the years. (I don't know if there is any time limit in the Philippines. In my home country it's 10 years.) So the mother would LOSE much money by that.

What does the signed agreement say?
If the lawyer was clever, it's included a text about you being the father, and if you aren'tm then the mother have done an additional crime I believe by signing you are the father...