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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.

Tried 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?

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In the future, if you use a blank site template and decide it's not correct because of missing features, just enable the missing features ;). I don't believe there's anything in the site templates you cannot activate afterwards on a blank site template. –  Cameron Verhelst Mar 6 at 6:24
    
I believe that the subscribing sites somehow have the CT HUB configured, correct ? Either as an associated service app or through a special feature they need to have activated. Removing any of these, would that have stopped the CT's from coming back ? –  Cameron Verhelst Mar 6 at 6:25
    
I was unable to activate the features i needed :( Managed Metadata being the main one. I actually got a null reference when trying to activate it with powershell. No i don't think the subscribing ones do, only the publishing one. published content types go to ALL site collections in the farm, i believe. or at least, any site collection with a web application with a subscribing timer job running. i suppose i could have disabled the timer job, but that wouldnt have fixed my problem of needing a new CTH –  Nacht Mar 6 at 21:26

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Turns out I had to bring the old content type hub back, but I didn't have to use my backup. The old site collection was still in the database, as an "SPDeletedSite"

I took a backup of my new CTH using backup-spsite (though ultimately unnecessary), deleted the new CTH, and used the restore-spdeletedsite powershell command to bring back the old CTH. i then unpublished each content type i had previously published, and then deleted the old CTH again, and used restore-spdeletedsite to bring back the new CTH.

I still do not know how to remove orphaned content types once the original CTH is completely gone... Sounds like they stick around for 30 days. After that, I'm pretty sure you'd have to create a new Managed Metadata Service to fix this.

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