The commit that fixes bug 851831 changes the name of the patch tarball used in grub-2.06-r2.ebuild, but the ebuild was updated without a rev bump. This seems to break the local distfile cache. When I ran `eclean-dist --deep` after my sync and @world update it deleted the old patch tarball, but the new one was never fetched since the package itself wasn't updated. Commit in question: https://gitweb.gentoo.org/repo/gentoo.git/commit/sys-boot/grub?id=830e49d291888e4d9ef8fec431a104f7cf9d1e21
I think gentoolkit should inspect the vdb to figure out which files to keep.
This is obviously not a bug in the grub ebuild.
I don't even think this is a bug in gentoolkit: to reinstall grub, you will need the new distfile not the old one. emerge will fetch the new file at that time.