Andrew, if you are using a default install, you can safely delete "everything" in your ZenCart directories. Then you just reupload the files from your computer. That is the quickest and surest way, to get rid of any unwanted files.
If you are using a custom setup (template overrides) you should already have current backups of those files. Reuploading those should put you back to where you where before all this started.
Note: two files you should make sure you have correct backups of are:
includes/configure.php
admin/includes/configure.php



