The plugin still exports the pinning information while it's not being used anymore since Jenkins 2.x (https://wiki.jenkins.io/display/JENKINS/Pinned+Plugins).

This field makes the plugin's output slighty different from the https://github.com/jenkinsci/plugin-installation-manager-tool input. Currently the plugin-installation-manager-tool is handling the issue correctly:

Invalid URL not-pinned , will ignore

This doesn't mean it will keep doing so, as the not-pinned field is not used anymore, let's simply remove it.