You can always loop through the array and skip all fields except for the one with the name you are interested in. For example, this example will loop through all custom fields and skip all where field.label is not Notes.
{% for field in custom_fields %}
{% if field.label != 'Notes' %}{% continue %}{% endif %}
<div>{{ field.label }}</div>
<div>{{ field.text }}</div>
{% endfor %}
When you go to Settings, then Custom Fields, is the custom field on invoice you are referring to set to be displayed on printed documents? If it’s not, then it won’t be available in custom_fields array.
I’m actually going to make Notes as a custom field. The theme is already assuming it is.