What does <span id="NWRTEReference[number]"> do in emails and is it an absolute must to have them seeing that Nintex automatically includes this markup whenever a control is added, and does not clear them every time a control is removed?
yes they are automatically added/maintained by nintex.
but they usually do not cause any problems. as far as body markup is valid HTML code you shouldn't see them in mail body (in mail client).
however, there are known annoyances so that when you edit a body in reach text editor, underlined markup is not updated respectively. eg. you delete a line from body but its enclosing paragraph tags are not deleted.
so you may experience something similar - you likely deleted a variable reference and its enclosing span tag didn't get deleted.
if you are sure it's orphaned piece of markup you can delete it in source editor.
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