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Backup initial sync

Backup resync never completes

Iam trying out to backup resync one of my application shard in production using Ops manager, but it is restarting in the middle with a rename collection exception and the resync never complete from 3 weeks. The collection in the source database is renamed by application process $out aggregation. The Mongo support says the $out should be stopped in order to complete the initial sync. But the app team can’t stop the process at this stage. The initial sync is not completing how to handle this… Any help would be appreciated…