How to mark a table as pre-populated with postgresql logical replication
I was able to get this fixed using a bit of a hack. Basically, drop the table from the publication, refresh the publication from the subscriber, add the table to the publication again, then refresh the publication again, but with copy_data=false:


drop the table from the publication.

alter publication my-publication drop table only my-table ;

Refresh the subscription.

ALTER SUBSCRIPTION my-subscription REFRESH PUBLICATION;


The log lines seem to stop at this point. Good! 
Add the table to the publication.

alter publication my-publication add table only my-table ;

Refresh the subscription with copy_data (false)

 ALTER SUBSCRIPTION my-subscription REFRESH PUBLICATION with (copy_data = false);



This seems to work, though it seems like it'd be problematic on a table that was changing rapidly.

It'd be nice to put this in a transaction somehow, but the commands are being run alternately on the publisher and the subscriber, so I don't know how that'd work.