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The update-endpoint-group or UpdateEndpointGroup API can be used to both add or remove Endpoints. The contents of the property --endpoint-configurations is a list which must contain the end state desired endpoints ie if you wanted to add one endpoint you need to include the current endpoints and the new endpoint, if you want to remove an endpoint you supply an --endpoint-configurations list without the endpoint you want to remove and this will then remove the endpoint from the group
You might want to consider using cloudformation or other IaC tool as you might find easier to manage adding/removing operations
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Thank you for this most complete and excellent answer! To delete all endpoints in a group, calling update-endpoint-group with an empty --endpoint-configurations clears all entries -- exactly what I was looking for!
It would be nice if this removal process was documented in the cli/api docs, even if just as an example.