Of course.Certified copies are as good as originals..
if possible, change them, else wait for the challan and get the certified copy
Under the Law, there is persumption of genuineness of certified copy which is good as the original. Yes, you can pray to the court to replace the CTC copy with the Original as you will be requiring the original for various purposes. Pray to the court that you qill submit the original copy as and when the court requires it.