Hi! In general, if you are dealing with broken manifests, please don't just update Manifest files blindly because the checksums give also some security benefit.
Some comments for sabayon-distro: app-office/libreoffice-l10n-* for 5.4.0.3: old version, can be ignored or removed completely; dev-vcs/subversion-java-1.9.5: doesn't harm, I tend to leave one old version during a version bump (it gives a somewhat nice diff for example), and will remove this one on next bump, but if you'd like all 1.9.5 svn split ebuilds can be removed. In my opinion, how fixing can be done: if you have several similar but not too big changes, they can go as one PR, to have better visibility on what's being changed for easier review and future reference. For example, removing several small packages can go in one PR; but removing all KDE l10n packages (it's just an example) I'd put in a separate PR. Alternatively, all this could be one PR but with changes grouped as above by commits.