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The purge interval for deletion stubs is 1/3 of the number of days for "Remove documents not modified in the last X days" in the database's replication settings. Try cutting this setting down to a smaller value. Note that there is a risk that if you make the purge interval too low, some deleted documents from servers or users that have not replicated since before the start of the interval may come back to life. (Your risk is highest if you have users who delete documents in local replicas, and then don't replicate with the server for many days.)
Before you do anything, make good backups. Then make sure that you replicate with every single server. Then follow the procedure in this IBM technote: http://www-01.ibm.com/support/docview.wss?uid=swg21095683. Then set the purge interval to the smallest value you can get away, and replicate again with every single server.