Removing domains, letsencypt clean up How to if needed

Yesterday I went through and did a lot of “clean up” on my mess that I made of a Yunohost server.
My home internet went out overnight and (as I usually get when it goes out) I got a lot of of cron email about dyndns updates. Some of them were for domains that I had removed earlier. I also got a letsencyrpt renewal attempt for a domain that was removed along time ago.
Is there a way to clean these up on dyndns and letsencypt where I’m not trying to renew domains that are no longer there?
Or should I just blow it all away and reinstall? Would I still be able to keep my current I use that email exclusively now.

I know on a desktop distro I’ve reinstalled without losing data by just reinstalling the latest image from a usb over the one that was installed. Is that possible without loosing my email?

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