Make sure you replace
the existing entries (not simply add these new ones). I have some 3rd party repositories that I use, but I have come accustomed to making a backup of source.list and then replacing everything in the file with the new entries (in this case incoming update pack 5). I've done the "manually merge the new lines and delete the applicable old ones" in the past, missing one or two along the way, and results were disastrous when doing a dist-upgrade
Even if your eyes think you caught all the conflicting entries, if you have a screen-full of them, it's best to start with a clean sources.list, do your upgrade, and then retrieve entries one-by-one from your old source.list file into your new one.