When invoking rsync, gensync appends "/*" to the repo URL producing a URL such as rsync://repo/overlay/* For some reason, the * completely changes rsync's behavior and breaks the --delete option -- as a result, ebuilds that have been removed from the upstream repo are not deleted from the local disk.
Created attachment 105401 [details, diff] fix
gensync has been deprecated in gentoolkit-dev-0.2.6.2 and will be completely removed in the next version.