I don't think there's nothing you can do to restore your working copy into its previous state, apart from doing it manually as you already mention.
Whatever, it isn't clear to me why your working copy contains a manually maintained list of files in older revisions. If those older files are required for current build, anyone else who checks out from the repository (including an automated build process) will systematically obtain the wrong files. Your repository actually lacks some information about current project version.
Is it possible that you actually want those packages somewhere else such as a vendor branch or an external, so that the HEAD revision contains automatically the required versions?