We have hit this error again, and we plan to snapshot the database as to be able to do whatever troubleshooting we can.
I am happy to report that we were able to get replication working again by running snapshots of the systems in question on servers running the latest point release 9.6.10, and replication simply works and skips over these previously erroring relfilenodes. So whatever fixes were made in this point release to logical decoding seems to have fixed the issue.