WQDS does accept Items from Wikibase anymore dues to conflicting URIs. WDQS is configured to accept the http://wikibase/ prefix, while Wikibase reports the (correct) https://wikibase.example.com/ prefix.
wdqs-updater-1 | 09:35:44.306 [update 0] WARN org.wikidata.query.rdf.tool.Updater - Contained error syncing. Giving up on Q1 wdqs-updater-1 | org.wikidata.query.rdf.tool.rdf.Munger$BadSubjectException: Unrecognized subjects: [https://wikibase.example.com/wiki/Special:EntityData/Q1, https://wikibase.example.com/entity/Q1]. Expected only sitelinks and subjects starting with http://wikibase/wiki/Special:EntityData/ and [http://wikibase/entity/] wdqs-updater-1 | at org.wikidata.query.rdf.tool.rdf.Munger$MungeOperation.finishCommon(Munger.java:800) wdqs-updater-1 | at org.wikidata.query.rdf.tool.rdf.Munger$MungeOperation.munge(Munger.java:413) wdqs-updater-1 | at org.wikidata.query.rdf.tool.rdf.Munger.munge(Munger.java:144) wdqs-updater-1 | at org.wikidata.query.rdf.tool.Updater.handleChange(Updater.java:436) wdqs-updater-1 | at org.wikidata.query.rdf.tool.Updater.lambda$fetchDataFromWikibaseAndMunge$7(Updater.java:286) wdqs-updater-1 | at java.util.concurrent.FutureTask.run(FutureTask.java:266) wdqs-updater-1 | at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) wdqs-updater-1 | at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) wdqs-updater-1 | at java.lang.Thread.run(Thread.java:750)
TODO: configure WDQS to use public WDQS hostname as prefix / concept URI.