The encoding of the URL is expected browser behavior - RadEditor's content area is an editable IFRAME and it is extending the browser's default RichText editing engine. For the time being we do not plan to change this behavior.
You can find more information on the subject in the following articles:
HTML URL Encoding Reference
As a workaround for your scenario I suggest you to find and replace the encoded string (%7E) instead of the exact symbol (~).
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