@richardwpg: Manually is an option for once or twice, but updating all those packages manually from now own isn’t really an option, thanks for the reply though.
@frederick: No errors in the logs, sadly.
Anyway, I’ve fixed the issue from now by switching to nginx, a planned change I was moving in front of me for a long time anyway. So seems to me, that this was an Apache error, maybe some changes in .htaccess that broke the update mechanism…