Please see the Example :
At your End:
You have taken ITC agst.Supplier Invoice No.01 ₹ 1000 in GSTR3B of June 18
You have Reduced The ITC agst.Supplier Invoice No01 ₹ 1000 in GSTR3B of July18
Finaly Net effect of Credit agst Supplier Invoice No1 is ₹ 0
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At Supplier end :
Supplier Issue Invoice No 01 in June 18 & paid GST ₹ 1000 in GSTR3B of June 18 & Upload The Invoice in GSTR1 return of June18.
Next Month Supplier have issued Credit note agst Invoice No.1 & Reduced his Liability of GST by ₹ 1000 in GSTR3B of Month in which Credit note is Issued & the same Credit note is uploaded on GSTR1 Return. The Net effect of GST is Zero at the Both end.