Eway bill missed

Eway bill and einvoicing are not related to each other in any way. Both are required in different circumstances. If both e-invoicing and eway bill are applicable to according to their conditions then both have to be generated. 

In your case since you have already dispatched the goods without eway bill you can still generate eway bill if it is in transit however you will face problems with dates. If the goods have already reached destination then you will not generate eway bill. That will remain a non compliance from your end.

Einvoicing is mandatory if applicable otherwise the invoice issued will not be considered as an invoice at all.

You will have to generate irn as soon as possible.