First off, to find all of those tags, you should check get_xpath:

my @foots = $document->get_xpath('//text:span[@text:style-name="footno
+te reference"]');
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Rather than using subs_text, you may just want to use set_text to set the text to whatever you've already figured out. But I think your idea is sound - you want to remove some text from one side, and add it to the other.