Not sure about just deleting CBTs in the CBT pod for a project - I think that you can just delete them if they aren't used anywhere.
Wishlists can be done here: https://www.adobe.com/cfusion/mmform/index.cfm?name=wishform
If you delete a tag from the CBT pod, you will get this message. I think it answers your question. I just tried it in a simple three topic project and it removed the tag from both content and topics. Nonetheless, I would take a copy of a live project before doing it for real.
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RH9 has the option to delete conditional tags from the CBT pod (image below). When you click Delete, it gives you the message Peter mentions. We've used this feature and it hasn't broken any of our projects yet (and we have some pretty big help projects).
However, as suggested, you must make a copy of your project before you delete all tags, just in case. Also, if your project is in source control, I suggest checking in your project files, and then again checking out your *entire* project folder before making a project-wide change such as this. If things go wrong, you can always just discard the check-out.
Thanks Peter - this was very helpful!