A third bug due to Archlinux' non standard way of installing doku.
You should consider reporting the bug to Archlinux. See
In the mean time, You can probably run the manual indexer. See https://www.dokuwiki.org/cli#indexerphp
Be sure to run the script under the webuser account (use su or something similar).
You may also modify your import script. Just after SFTP is done, use curl to trigger the indexer. For example, if you need to index some:page, the curl command would look like this (assuming an sh script) :
curl "http://your.doku.server/base-doku-path/lib/exe/taskrunner.php?id=some%3Apage&$(date +%s)"
The data plugin does not use the indexer. I think the db is updated when the page is viewed for the first time.
So after calling taskrunner.php, just get the page with curl, ie something like this:
Using curl with authentification on a closed wiki will not work right away. You can use a browser to log in your wiki, and then tell curl to use your browser cookie file. curl -b /path/to/your/cookie/file http://....
. See curl manpage.