Comments aren’t in the “footer”, they are in the Loop, and they need to be to keep their association with the parent post. That is why you are having trouble. You are moving them out of the context that Core expects. What you are going to have to do, I think (and I haven’t tested this), is explicitly pass the post ID to the relevant functions– comments_open() and is_single().
if ( comments_open($post->ID) && ! is_single($post->ID) ) :
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