I am sure many have already done this, but if you haven’t yet, you should, as support for the MS Exchange Protocol ends by the coming weekend. You can read about when Microsoft announced this change back in February 2024.
You will not see the warning in Dynamics if you have not set the Batched Emails Protocol to Exchange, as shown in the next picture.
However, you should remember that individual users have the option to configure it as they wish, and they can change it if they want, as it is in the user options.
You will need to register an app on the Azure Portal, as documented. Once you have the App ID and Secret, update the settings and test the communication with Microsoft Graph using the link on the form.
Once you verify that MS Graph is working, enable/activate it by moving it from the left to the right. It will look something like this.
At this point, for all the users who are using Exchange for their emails, update them to MS Graph.
You might get tired of doing this for hundreds of users, so using an Excel Add-in or something similar can be helpful.
Once users are updated to MS Graph, go back and remove the Exchange Protocol.
First, remove it from the Batch Emails Settings and then turn it off by moving it to the left.
Your final step is to check the history of emails from the point you started working for this change until now. If any emails failed while you were switching, clear the errors by clicking "Resend." This can be done from the email history.
I was looking for the same on the CE/Dataverse side and wasn’t able to find the availability of MS Graph there (as of today).