Dear Vignesh Ji,
Mismatch or difference does not mean you have caused any loss of revenue. You will have to justify the difference between both returns with documentary evidence based on books of accounts. You know books of accounts are a statutory records. You must have following genuine documentary evidence / docs :
1. Physically receipt of goods in the registered premises before taking ITC as required in terms of Section 16 of CGST Act.
2. Valid tax paid invoices.
3. Proof of payment of tax by the supplier.
4. Proof of payment of value of goods/services to the supplier.
Have you any doubt about legal validity of the mode of payment done via bank transfer ?
If your client conforms to the parameters laid down in Sections 16 & 17 of CGST Act, ITC cannot be denied. In this way, the availment of ITC will be within ambit of CGST Act and NOT beyondGST Acts.
You can prepare reply to SCN or simple notice accordingly.