1) The certified copy obtained from the Sub-Registrar office is a valid document. However, u hv to verify whether the last page containing scheduled property shown now by the seller is not tampered and exactly the same as the original.
2) U may check online thumbnail documents from the SR portal if loaded or otherwise obtain another certified copy keep it for yourself which will be useful as a link document in all ur transactions. Do not ask the seller to provide u with another certified copy but u should apply by urself not the seller on your behalf to avoid tampering if any in between.
3) A suitably drafted affidavit to that effect be obtained from the seller. Get the same drafted by an experienced civil lawyer of your area.