MarkLogic's documentation (pre-ML9) on database replication warns users against this, stating that:

You cannot replicate a Master database that acts as its own schema database. When replicating a Master schema database, create a second empty schema database for the Replica schema database on the Replica cluster.

What happens if I attempt to do this?

In earlier releases of MarkLogic Server, this has been known to cause cluster outage and several support cases have been raised due to this configuration causing undesired - and unexpected - results.

In newer releases of the product (such as MarkLogic 8.0-5 and above), the Admin GUI on port 8001 and our admin APIs will now stop users from making this configuration change in the following ways:

• In the Admin UI on port 8001, setting up replication between clusters and configuring database replication for the Schemas database should now fail with the message "Cannot setup replication for a database whose schema database is itself"
• Using the Admin API with a call to error 2. Couple a cluster and call to admin:database-set-foreign-master against the Schemas Database should fail, instead causing an ADMIN-DBREPSCHEMADBSAMEASDB exception to be thrown.

This is still an issue for MarkLogic 7 and earlier releases, so it's important to always ensure that you are using a separate database for your replica as advised in our documentation.

Best Practice: Always separate out Schemas Databases where necessary

If your application makes use of Schemas, create a completely separate schemas database for your application.  Doing this keeps your application self contained and allows you to replicate it as you would with any other database.