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Thank you for re-posting to this forum.
Was this a bug in Bdb4 which got fixed in Bdb5 or is this change unintended?It is a bug fix in JE 5. Previously, changes to the database config were not replicated. The exception is thrown because at attempt to change the config is being made on a replica, rather than the master.
Are you enabling key prefixing on the replica, when it has not been enabled on the master (or perhaps the change was made on the master but not yet replicated)?
The other possibility is that this is a duplicates DB and there is a more subtle problem related to the fact that JE 5 automatically enables key prefixing for duplicates DBs. Do you call DatabaseConfig.setSortedDuplicates for this database?