We have recently worked on a project where a customer decided to remove hybrid content types configuration and control all the content types from on-premises Content Type Hub.
Stop-SPContentTypeReplication cmdlet was used to stop the content types replication. This has removed the replication between environments. The required content types were then recreated in the on-premises Content Type Hub and published.
We then moved with the project and started creating site templates to support the agreed design. What we noticed was a discrepancy between some columns in the Content Type Hub and in the newly created site collections. After a short investigation, we found out that there were a number of content type publishing synchronisation errors and conflicts. At this point it became clear that when Stop-SPContentTypeReplication was run, all SPO published content types were copied to the on-premises Farm but were invisible in Content Type Hub. This prevented us from being able to un-publish them from the on-premises CTH.
The way we resolved the issue was to un-publish all conflicting content types from the on-premises CTH, rename them and re-create them with ID’s matching the content types in SPO. We then published and un-published them. That has removed the orphaned SPO content types and allowed us to publish the on-premises content types.
This issue could have been avoided by unpublishing the SPO content types before running Stop-SPContentTypeReplication cmdlet.