I found this bug a few days ago and my memory is a little fuzzy, so pardon me if I'm not 100% accurate.
On line 592 of function_mail.inc:
For some reason the $data variable is populated a different way when deleting an event, and thus this section of the code does not display the custom fields when sending email.
adding the following to line 593 fixed it for me. I'm sure there's a more elegant solution.
591 $key = $field['name'];
592 $value = (isset($data['custom_fields'][$key])) ? $data['custom_fields'][$key] : '';
593 $value = (isset($data[$key])) ? $data[$key] : '';