Only two months after the involuntary absence of bugzilla.netfilter.org (due to database corruption while doing a gentoo mysql update), I have finally found some time (and a way) to fix the problem. Therefore, as of today, bugzilla.netfilter.org is now up and running again.
This was possible due to the fact that the bugzilla tables were still present in myISAM format. The mysql tables of patchwork.netfilter.org were not that lucky. They were stored in exactly that InnoDB file that got corrupted. However, the loss of archived (and lots of unmaintained) information on patches that had been submitted on netfilter-devel is not really all that important anyway.
However, let this be a lesson: Do daily dumps of all mysql tables in a cronjob before doing backups ;)