As you hadn't changed anything in Zen Cart and were referring to emails generated by orders and (I assume) from the contact page (i.e. two completely different parts of Zen Cart's code), this sounds more like a problem with your server environment and specifically your mail server.
Do you have any other applications on your server that generate emails (other than that which you usually use to send emails from your desktop which is usually different) and if so, are they still working and which mailing method do they use? You may want to ask your web host whether other people have reported similar problems.
(and put the other files back how they were, it's unlikely that they're involved)
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