Can Blockcerts be used with R3 Corda?

Not natively no, you will have to develop your own transaction handler for this blockchain.

I have not worked much on direct development of the issuer, so I am not sure what pieces are needed, but here is the entry point where the decision is made for which blockchain handler to use: cert-issuer/issue_certificates.py at master · blockchain-certificates/cert-issuer · GitHub

With that you should be able to identify the flow.

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