Most queries should run fine on the appropriate graph (main vs scholarly), but for queries that must run across the full dataset, the queries must be (re)written to use SPARQL federation [2]. You can ask for help to rewrite your queries [3]. If you encounter issues please feel free to report a problem [4].
If you need more time to do the transition you can use the new legacy endpoint [5] (query-legacy-full.wikidata.org) which contains the full Wikidata graph, but is limited in terms of performance and availability. Please be mindful when using this legacy endpoint and use it only if really needed. This endpoint will be available until December 2025.
We are moving to this next stage on Monday May 5 (2025-05-05).