Is the sale of deed valid if it is stamped but made in 1973

My grandfather entered into a sale agreement of agricultural land in the year 1973 without section 43 permission with a silk mill company. The same agreement is duly stampduty paid as well as registration stamping is done reading year 1973 and and pages no , but last page there is a remark of sub registrar stating Registration is refused as the parties did not admit execution within the time allowed as per registration act1908, LATER after 3 years Deed of confirmation is registered and no stampduty paid in year 1976 by the parties stating they admit execution for 1973 agreement which they failed to do in 1973, IS this Sale Transaction LEGAL as stampduty was paid in 1973 and admit execution through Deed Of Confirmation in 1976