A taxpayer have to file different GSTR 3B for each GSTIN registered on his business organization...
Also as per section 25(4) of CGST Act, If a Taxpayer has obtained multiple GST Registrations whether in one state or more than one state, it shall be treated as a distinct person & in respect of each such registration, GSTR-9 is required to be filed separately for each such GSTIN.
So as per above clarification you'll be required to file different GSTR 9 for each business registered in different state.
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