In SP 2013 on-premise, I have created a site collection for Content Type Hub, and one for Intranet. The content types are synchronized to the Intranet Site Collection from the CT Hub.
I did some changes to Content Types in the CT hub, i.e change parents and ID's. Of course that would put me in serious trouble, and it did. So I deleted both the site collections, and re-provisioned Content Type hub and content types with new ID's etc, and I also re-provisioned the Intranet Site Collection. While the CT Hub site collection seems to be update, the Intranet Site Collection gets Content Types that are deleted, and old content type stuff.
I have deleted site collections, and re-provisioned. I also run all the timer jobs several times, i.e the Content Type Subscriber and Content Type Subscription jobs.
Is there any thing else I can try?