I have a Shopify Application with several thousand installs.
I recently moved the application hosting from Heroku to AWS. As such the URL for webhook for all endpoints have changed (from skuharmony.herokuapp.com to api.skuharmony.com). Upon moving the hosting, I updated all webhooks for Shopify stores for which I have permission to the new endpoint.
However, I'm now getting occasional emails from Shopify with the subject "Your webhook is failing". The email indicates it is for a store that has uninstalled my application. Shopify Partner Delivery Logs indicate it is for "shop/update" webhooks, so it is a result of the store has updating something.
This appears to be a bug that the webhook for my application would still fire when the store has uninstalled my application. I have no ability to change the webhook, and no ability to "redirect" the request being send to the herokuapp location.
I've taken a look, and from what I am able to see, this may be occurring for frozen or paused shops that still have your application installed. You can check the webhook delivery logs in your partner dashboard to make sure it's the old address that is being called and failing, but otherwise you should be able to safely ignore the emails.