I’ve hit the same problem with a ContentView only containing SLES repositories: New CV versions with SLES repos do not contain (all) errata after Pulp-Migration
It is also a regular ContentView (no composite ContentView), but had one filter applied. As a result the new versions had 18 errata (instead of ~4600). After removing the filter, the published version contains all errata again.
So this problem seems to not only affect EPEL but also SLES repos (at minimum). We also do have EPEL and RHEL content, but those CVs do not use any filters; so I don’t know if we would have the same problem there (probably yes).