The time may come when you need to take a content type out of circulation, or it may just be because you made a mistake and need to replace it. Whatever the reason, if this content type is defined in your content type hub, circulated via content type publishing, then consider the order of operations before clicking buttons.

The content type in question in the subscribing site collections will have one of two outcomes when it becomes unavailable in the content type hub:

1. When a published content type is deleted, it will remain available for download for all site collections in every web application that consumes content types from the content type hub. Any copies of this content type will be orphaned.
2. When a published content type is unpublished, it will become unavailable for download for all site collections in every web application that consumes content types from the content type hub. Copies of this content type being used in subscribing site collections will be unsealed (set to not be read only) and made into a local content type. In no situation will the content type be automatically removed from any subscribing site collections.

Why does deleting not have the expected effects like unpublishing? Once a content type is published, that content type definition for subscribing is actually stored in the term store database for the managed metadata service of which the content type hub belongs to. The only way to change the content type definition is to manipulate the content type in the content type hub and re-publish, causing an update to that item in the term store database and thus updates to subscribing site collections’ sealed copies. The nature of this structure means that, if you were to delete the content type from the content type hub without first unpublishing it, all copies of the content type in subscribing site collections will become orphaned–they will lose their ability to be updated while still thinking that they are subscribed. In fact, when a new site collection is created that utilizes that content type hub, that orphaned content type will appear because it is being retrieved from its item in the term store database. You will never be able to unpublish an orphaned content type, unless you follow guidance from this blog post.

So, the workflow must be:

1. Unpublish the content type.
2. Delete the content type in the content type hub.
3. Optionally, clean up unsealed copies of the content type in the subscribing site collections.

P.S. – Keep in mind that any site columns from the content type hub that were associated with the removed content type in question went along for the ride when it was published. They do not get retracted–unpublishing leaves these site columns behind in the subscribing site collections as well.