I solved the problem myself.
Seems like either the initial sync or metadata generation caused some half-baked repodata files.
The following steps resolved the problem:
- Validate Content Sync for the broken repo
- Verify Content Checksum on the broken repository (just to be sure)
- Republish repository Metadata on the broken repository (just to be sure)
- Republish repository Metadata on the broken Content View versions
During troubleshooting, I also applied the following two patches as I saw some errors related to them. Maybe these patches fixed the root cause which caused the broken repo in the first place (not sure about that):
Now, the repository contains all previously missing packages and all clients can update successfully.