I've struck this bug 3 times now with the Sep 22 build, different machines, different PBIX files. When I open a PBIX file with Query Groups, the queries that were in groups have all been moved into t...
The exact same thing happened several times with me.
I noticed a pattern. I'm working on a query (SAP BW) to which I don't have appropriate authorization. So I did the requested changes and saved the file, closing the query editor without applying, and saved in SharePoint for a colleague that do have the authorizations but not the PBI expertise to apply the changes.
When he downloaded the file though, the query folders and load/not load status was gone from all queries (quite a few queries are staging only and not loaded to the file). I checked my copy after saved and synced with the cloud and it was the same thing.