This warning is only displayed when one of the addresses in the order has a country which is not found in the Zen Cart database. This is an extra check which was added to warn administrative users. When the country cannot be detected / determined by Zen Cart, tax and shipping calculations may not work correctly.
What is the country listed in the order (in the order db table) for "customer", "billing", and "delivery"? Does it match exactly (including case) the name of the country (in the country db table)? Are both tables using the same db collation?
Some 3rd party modules (such as minimum customer info) do not populate the country fields when creating an order (which also results in the country not being found). If you are using one of these you can ignore the warning... Or fix the 3rd party modules code to add the country to the addresses in the order...
Edit Orders does not automatically send emails to customers when you update order details such as the address, products, or order total lines.
In Edit Orders 4.1.2 when an administrative user enters a comment AND changes the status of an order the comment is saved to the database. If when the comment was saved AND the administrative user selected notify customer via email, then an email will be sent to the customer's registered email address. So if one adds a comment and changes the status of the order from "pending" to "quoted" and selects notify customer via email, then the customer is sent an email letting them know the status was changed to "quoted" and includes the comments.
There is
a patch posted earlier in this thread outlining what change needs to be made if you want comments to be saved when the status of the order has not been changed. The change is already incorporated into the next release of Edit Orders, but if one wants the change before 4.1.3 is released they need to manually apply the patch.