Due to critical issues, we have temporarily deprecated the merge command in cbbackupmgr from versions 4.5.x and 4.6.x. We plan to fix those and re-introduce support for the command in the upcoming Couchbase Server 4.6.3 and 5.0 releases.
We found that a DCP rollback during backup can cause issues later when the merge command was run. Scenarios such as database purging, bucket deletion and recreation, and bucket flush can cause a rollback. To track this issue in JIRA, see MB-20403