DIFFERENCE TAX LIABILITY BETWEEN GSTR 1 & GSTR 9 - Goods and Services Tax - GST

Sir, When the Taxpayer has filed their GSTR 9 they had put up actual value of outward supply as per books by deleting the auto populated value which comes from GSTR 1 in column no. 4(A) and GSTR 9 was rectified accordingly. So no chance to reconcile GSTR 9C in column no. 9(R) as GSTR 9 was already rectified. Now my question is that at the time of audit whether Dept can further demand the tax after reconcilation/rectification of GSTR 9 / GSTR 9C ?