no, you won't because tax laws bar you from switching from a joint return to 2 married filing separate returns. (the other way is allowed - MFS to joint)
however, nothing prevents you from doing the calculations as if you were amending.
several rules should be followed since they would apply if originally you had used MFS.
1) if you're both the parents then the one who has the right to claim them is the parent with whom they lived the greater portion of the year (temporary absences ignored)
2) if 1) is a tie then the parent with the highest Adjusted Gross Income gets to claim them
3) both must itemize or use the standard deduction
if you got a refund on a joint return it is up to the two of you to agree on how to split the refund.
There is no reason to amend.
If you had filed MFS you probably would have a smaller refund combined.