As far as I can tell, these four RPMs are also the only packages located under Package/ without the trailing s. This makes it seem likely that the files under Package/ are either outdated or were not intended to remain there.
This causes issues for tools such as Red Hat Satellite or Pulp (standalone) when mirroring the repository for offline use. They detect these as duplicate packages and fail during repository synchronization.
Is there a specific reason why these four packages are available in a separate Package/ directory as duplicates?
In our case (we use Red Hat Satellite), it is not possible to ignore specific paths. The initial sync fails as early as the metadata parsing stage because duplicate packages are found, which should not happen.
I’m not sure, but the problem would likely occur with any other software built on top of Pulp as well.
After removing the duplicate path and uploading the RPMs directly, Pulp/Satellite generated metadata successfully and the repository worked normally.
So the issue does appear to be specifically related to the duplicate Package/ entries present in the upstream repository metadata.
One additional note: this workaround takes quite a long time, especially during the upload-content step, since Satellite/Pulp processes RPMs individually. However, the process completed successfully and allowed us to publish the repository normally.