Did you get the Zen Cart logo properly before you started making changes? If so, then you have likely messed up the path/filename combination during your updates. If not, then perhaps there's a permission problem in serving the file. Is your logo a jpg or gif? or some other format?
Does your server errorlog show any errors when you attempt to read the email that contains the broken image?
What does the email's raw HTML content say? It should show the path and filename clearly.
What email program are you using? Outlook loves to block graphics until you tell it to show them, thinking it's doing you a favour (and it sometimes is).
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