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Not to Necro this discussion thread, but had a similar issue after deleting identities when we wanted to move to using a domain. Since we couldn't use the Cognito User Pool config to update the Identity (we had more than 100 and that causes some bug on AWS side in loading the dropdown)
Used the CLI to update the User Pool email config using your example would be:
aws cognito-idp update-user-pool --user-pool-id {userPoolId}
--email-configuration "SourceArn=arn:aws:ses:{region}:{account}:identity/{domain},ReplyToEmailAddress={emailInDomain} ,EmailSendingAccount=DEVELOPER,From={emailInDomain},ConfigurationSet={optionalName}"
Funnily had to temporarily disable advanced security (we were in audit only) in order to be allowed to perform the above update. Success after.
Would be nice to get a warning when deleting identities that they are in use elsewhere.
Edit: Warning not providing values for other config will reset any Custom lambda triggers on Auth or your Messages so make sure to take a good look at your config before running the above.
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- asked 4 years ago

Having the same issue but for eu-west-1, I have used this email before so not sure whats going on.
I also am experiencing this. On top of what is said above. If you use boto call to list verified identities, https://boto3.amazonaws.com/v1/documentation/api/latest/reference/services/ses.html#SES.Client.list_verified_email_addresses, they do not show up in the response list. So they show in the UI as verified, but not via an api call.