Excess refund of income tax

Return is filed u/s 139(1) and the same is also revised u/s 139(5). However before receiving ITR ack. of revised return dept processed return on the basis of original return & granted the refund Afterwards the dept received the Revised Return Ack in which refund was reduced. However revised return was uploaded before processing the original return on the basis of which dept sent the intimation u/s 143(1) granting higher amount of refund. What will be the consequences in this case?