Basically, because you're doing something that's not really supported (copy a snapshot of the repo and rename it). In order to support "shadow" repositories, like sabayon-weekly, where the only content that differ from the original sabayonlinux.org is the database/ directory, the original repository identifier from where a package comes from is recorded into the sqlite3 database itself (packages.db) the EntropyRepository.getInstalledPackageRepository() method. See https://github.com/Sabayon/entropy/blob/master/lib/entropy/client/interfaces/package.py#L547 However, it should try both the original and the current repo paths.
I am not sure, but changing the "product" information in entropy config files (/etc/entropy), and renaming the directory remotely might be a better solution (if it works for you). -- Fabio Erculiani