Upon further checking my claim made above, noticed that this problem does not only not occur on Wikidata but also it doesn't occur on two other WB instances I manage (both non-WBC and with different technical setups). This makes it look more like a WBC specific problem and not a general one. In my post above, I only assumed it would effect Wikidata as well, considering that this looked like a general communication issue problem between SPARQLWrapper and the query service. I didn't thoroughly check it. Sorry for the confusion there. I updated my comment accordingly.

This is kind of a shot in the dark, but I remembered an issue we had a couple of years ago, that might be useful here. A bit of context: We had a manual installation of Wikibase (without the docker image, because it wasn't available back then). Later we installed the query service via the docker image and made some manual adjustments for the URLs in runUpdate.sh . It worked fine for a while but at some point the updater broke and we didn't notice right away. After some edits a while later we noticed, got the updater running again, but the new items still wouldn't appear. IIRC the cause was that the updater would query the recent changes but since the last import into blazegraph was more than 90 days ago, it didn't see the last point to connect to. The fix was just to increase the $wgRCMaxAge and run maintenance/rebuildrecentchanges.php again.

I found this ticket, because I encountered the same problem. But I have a bit more insights into the issue now, so I am posting it here, in case somebody else finds it the same way that I did.