Under section 143(1) (a) notice issued on business income

Business entity filed lady year income tax return delayed return as per section 139 (1). It return rejected and 143(1) (a) issued due to late filing the it return losses carry forward not accepted and ask us file the revised return. Now revised return how will adjust loss during the year not carry forward ITR- 3 where should be adjusted please clarify
thnks and regards
Subramanian S