To get rid of the portfolio file, you could just simply delete it and the folder that has the prettyPhoto file in your theme.
I’m willing to bet that it’s something else causing those errors, maybe some custom code, or a plugin of some sort, or bad WP install. The prettyPhoto plugin is not activated whatsoever unless you actually use the portfolio template. And even then, it wouldn’t do that. I’m not sure why they would tell you something like that, no other site has ever had this issue before in any theme. Who are you hosted with?
You can use FTP to delete the files, or you can make a copy of your theme and delete the files from your desktop, then rezip and upload. Either way will work (FTP is recommended).
If you can, please keep me updated, because I’m curious about this.
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