Hello,
No it would not affect any other certificate. Both the certificates that is migration certificate as well as domicile certificate is completely different. Domicile certificate proves the nativity of a candidate in a particular state where as migration certificate is to help you transfer from your old institute to a new institute to achieve higher education. I do not think that it would cause a problem as both are required for higher studies.
Hope it helps.
Good luck.
Regular exam updates, QnA, Predictors, College Applications & E-books now on your Mobile