I'm guessing that the part you're not telling us is that the text you're looking for is missing in the text-only emails, and that you're not referring to HTML emails, despite only editing the HTML email templates.
In v1.3.x, those files in the /email/ folder are ONLY for HTML-formatted emails.
If you want to change TEXT-Only emails, you'll need to manually edit the many different language defines in the appropriate checkout language file.
In the (not yet released, no date set yet) v2.0, the text and html emails will be handled from the /email/ folder, making it a lot easier to edit your email content.
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