If you are using 2.x version of couchbase lite clients, the “allow_conflicts” is always false (We should make that clearer in our documentation).
Conflicts in 2.x are automatically handled by the system and you have option to override it. More details in our docs. You must have push-pull replication - conflicts are resolved on pull. So when CBS rejects the document update with a 409, CBL will resolve the conflict and push up winning revision. This blog describes automatic conflict resolution - which of course you can customize as described in the doc link.
Tagging @ibsoln for documentation impact,