I’m going to suggest to the author that the following manual reset short code is added to the plug-in. When testing with my website, it fixes the problem without any side effects.
Then it doesn’t matter what the Theme does, it always works. For reference, I’m using the ‘color newsmagazine’ theme.
add_shortcode( 'efn_reset', array( $this, 'short_code_reset' ) );
/**
* Manually reset foot notes and counter
*/
public function short_code_reset() {
$this->footnoteCount = 0;
$this->footnotes = array();
return "";
}