I have created a Content Type Hub and several content types and published them.
Then I realised that I used the blank site template which won't work because it's missing several features, so I deleted that site collection and created a new one with the same URL.
I then noticed that the content types from the old CTH were still on the subscribing sites (of course). Tried to delete them but they came back.
Tried checking the checkbox for "Refresh all published content types on next update" but it didn't help.
Set-SPMetadataServiceApplication -Identity "Managed Metadata Service" -HubURI $hub.url to refresh things maybe, but it didn't help.
As a last resort I do have a backup of the old CTH, I can load that back up and unpublish. Is this my only choice?