RPM files deployed into hosted yum repositories do not always appear in the yum metadata files after Nexus Repo rebuilds the yum metadata (e.g., they are missing from the primary.xml.gz file).
This is an intermittent problem, but we've seen it enough now to conclude that this is a real bug. This Jira is entirely distinct from the specific symptom and solution documented in
Do a new code review the yum metadata rebuild code and address any minor issues found. Substantially improve DEBUG level logging in case the minor code changes still do not resolve the problems reported by customers.