Thank you for reaching out.
I understand you added a new backend setting and new backend address pool to your Application Gateway and this caused existing web socket connections for your other backend server to disconnect.
This is actually expected behavior for Azure Application Gateway as the update applied to Application Gateway are applied one update domain at a time. As each update domain's instances are being updated, the remaining instances in other update domains continue to serve traffic. Active connections are gracefully drained from the instances being updated for up to 5 minutes to help establish connectivity to instances in a different update domain before the update begins. This is currently documented here.
It is recommended to apply changes to the Azure Application Gateway during down-time or a maintenance window.
Hope this helps! Please let me know if you have any additional questions. Thank you!
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