Ok, I found the error.

The database for the indexer changed location to
"/home/patrik/.cache/zim/notebook-home_patrik_Documents" instead of
".zim" folder in "Documents". After removing the database from the new
location all was updated correctly.

/Patrik


On 2014-09-17 09:19, Jaap Karssenberg wrote:
> Hi Patrik,
>
> I'm on revision 729 myself and I do not see such an issue. Also there
> is nothing in the recent revisions that is related to the indexing. So
> no obvious place to look for this bug.
>
> Can you try "zim --debug" to check for errors in the debug output when
> you create the new page?
>
> Regards,
>
> Jaap
>
>
> On Wed, Sep 17, 2014 at 9:10 AM, Patrik Nilsson
> <nipatriknils...@gmail.com <mailto:nipatriknils...@gmail.com>> wrote:
>
>     Hi All,
>
>     Revision 729 (or some very recent) introduces a bug for the
>     indexer. The indexer forgets every subpage below level 2.
>
>
>     If you add a subpage below level 2, it disappears on restart. It
>     still exists on hard-disk.
>
>
>     Many of my pages are not accessible from zim anymore.
>
>
>     Best regards,
>     Patrik
>
>
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