Yum caches the repositories' filelist.xml. If your metadata is somehow cached forever, you can easily refresh it by clearing it manually. The cache files are located at /var/cache/yum/. So simply remove the repo name directory and that should trigger yum to repopulate the cache.
# cd /var/cache/yum
# rm -rf <reponame>
# yum update
Note: this is applicable for Fedora and CentOS/Redhat operating systems.
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