Hello
Thank you for your question and reaching out. I can understand you are having query related to IE disable.
If your Enterprise Mode Site List contains applications that are configured to open in the IE11 app and you disable IE11 with this policy, they will open in IE mode on Microsoft Edge.
In your case I will suggest you to Disable IE using group policy as per below guide.
https://learn.microsoft.com/en-us/deployedge/edge-ie-disable-ie11
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