To manually initialize a server when an online initialization isn't possible:
  1. From another server in the replication topology, back up the userRoot, schema, and replicationChanges backends to the <server-root>/bak directory.
    Tip:

    If data encryption is enabled, export the encryption-settings backend because you might need to import one or more encryption settings IDs into the new replica.

    $ source-server-root>/bin/backup --backendID userRoot --backupDirectory \
   bak/userRoot
$ <source-server-root>/bin/backup --backendID schema --backupDirectory \
   bak/schema
$ <source-server-root>/bin/backup --backendID replicationChanges \
   --backupDirectory bak/replicationChanges
$ <source-server-root>/bin/encryption-settings export --id <id> \
   --output-file bak/exported-key
  2. Copy the bak directory to the new replica. 
    $ scp -r <source-server-root>/bak/* \
    <user>@<destination-server>:<destination-server-root>/bak
  3. Stop the server.
  4. Restore the userRoot, schema, changelog, and replicationChanges backends.
    Important:

    If the encryption-settings backend was exported, import it before restoring any of the backends.

    $ <destination-server-root>bin/encryption-settings import --input-file \
   bak/exported-key --set-preferred
Enter the PIN used to encrypt the definition:
$ <destination-server-root>/bin/restore --backupDirectory bak/userRoot
$ <destination-server-root>/bin/restore --backupDirectory bak/schema
$ <destination-server-root>/bin/restore --backupDirectory \
   bak/replicationChanges
  5. Start the server using bin/start-server.