Does it happen all the time or sometimes?

If it's sometimes, it's like duplicate of T233520: Wikidata changes do not get sent to client sites on initial sitelink addition (in some cases), leading to things such as missing page props in page_props table

No page seems to know the sitelink. A null-edit does not help. The page_props table is empty for these page_id.
Is there a possibility to rebuild the page_props?

When setting the sitelink via pywikibot, the page_props table does not get changed as well.

Maybe the jobs are not being ran, Have you run maintaince/runJobs.php?

Ah, thanks for the hint. There is a problem with the job queue on our, but it might take some days until the queued jobs are done. I did not notice, that had to take care of the runJobs.php on my own.

Therefore I tried it with a fresh installation of containerized wikibase and after finishing the jobs queue, the page knew about the linked item. I've attached the code for populating the sites table with values, valid for the docker-compose.yml setup. It can be executed with the maintenance/eval.php script.

This clears the sites table, before adding the local site.

$sites = [];
$langCode = 'en';
$site = new MediaWikiSite();
$site->setGlobalId( 'my_wiki' );
$site->setGroup( 'wikipedia' );
$site->setLanguageCode( $langCode );
$site->addInterwikiId( $langCode );
$site->addNavigationId( $langCode );
$site->setPath( MediaWikiSite::PATH_PAGE, "http://localhost:8181/wiki/$1" );
$site->setPath( MediaWikiSite::PATH_FILE, "http://wikibase.svc/w/$1" );
$sites[] = $site;
$sitesTable = MediaWiki\MediaWikiServices::getInstance()->getSiteStore();
$sitesTable->clear();
$sitesTable->saveSites( $sites );

That's also important, otherwise it can't understand the repo. Should we call this resolved then?