the only issue we are facing with the new account reconciliation is we are unable to clear out our check voids by matching the corresponding JE

do you mean that it net out to zero? I only ask because we've had a few transactions that when matched have no value ie. Deposit and Refund on the backside and the corresponding payment and refund on the NetSuite side. NetSuite support advised to just lump it into another match that has an amount greater than zero.