I don’t think revocation is appropriate in this case unless you believe the private keys have been compromised by another party. If you’ve lost them and don’t suspect they are compromised I would just issue new certificates and allow the “lost” ones to expire naturally. Revocation adds load to our service and shouldn’t be used unless required.
With that said, on the server-side, since Boulder #2319 its possible to revoke an existing certificate by setting up valid authorizations for all of the contained domains using a new account key and then asking the server to revoke the existing certificate. Unfortunately I don’t think any ACME clients are exposing this functionality so it would be a complex endeavour to utilize it for your certificates.