After April 2019 the policy of “one invoice, one e-way bill” was been introduced embedded in the system too via making enhancements in the E-way bill portal. Prior to this, due to technical issues and the introduction of the new GST system, many taxpayers inadvertently generated two or more e-way bills for a single invoice. In such cases, you should respond with the actual invoice, the corresponding e-way bill, and any other supporting documents, providing a clear explanation for the multiple e-way bills. Hopefully, the GST officer will offer some remedies for this issue, which often arises from a lack of awareness.
You may write reply functionality of multiple generation of E-way bill on the same invoice was specifically blocked through enhancement in E-way bill system introduced in the month of April 2019. Prior to that the portal allowed generation of multiple E-way bills on single invoice. Hence the inadvertent error persisted due to non-availability of functionality. Hence punishing the taxpayer with the demand of tax in the initial phase of implementation of the GST law due to clerical mistakes, when the requisite functionality itself was not available is undue and harsh and therefore should be dropped.
I will also suggest take more advise with GST Expert.