lpm --sync --all

This command checks all default remote repositories and downloads the information about any new packages. --sync --all does not actually download or install anything. This command downloads the updated list of packages published by all remote repositories, and information abouy new packages.

--sync --all does not delete information about removed packages from the remote repository directory. Large primary repositories are mirrored, and occasionally some mirrors may not've been updated with new packages. The first --sync could've been routed to a mirror with new packages, and lpm would've downloaded the new package information, but the next -sync could've gone to a mirror that has not yet received the new packages. This is why information about missing packages does not get removed automatically.

lpm --sync --all --purge

Add the --purge option to remove information about deleted packages from the remote repository.