This problem appears to be solved for now after notifying the MongoDB support.
But some data is not available according to the GraphQL results. The data is missing from the date when we had a sync failure last week when we were trying to create a flexible sync app and it overloaded the cluster which is in the M10 tier. But earlier we could see the relevant data in the mobile devices which were syncing but not in the MongoDB.
We wish to upgrade to the M20 tier now since there are some sync errors as raised here: https://www.mongodb.com/community/forums/t/error-starting-sync/202872.
Any help is much appreciated.