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You can try to create a new Database with same design and use an server agent to copy each document from old database to new database to fix the problem.
ND10 with ODS53 extended the limitation to 15 times larger than ODS52,did you still met that problem?
I know that but is not a solution, -Replica not working on big databases. Is a bug that need repair. We don't have discution databases with 10 users and 100 document but milion of documents and over 10k users.
You have no choice except to run compact -Replica or pull a fresh replica from other server.