Error filter template : Email template '' is not defined
I couldn't fix the main issue, so this is what I did.
I made the "header" kind of extend to the email body. For example, order_email.html and added a CMS block call to there (I know, right!). Within the main admin area, I created a new CMS block and pasted the image (in my case) there. I made sure to name the block so I would be able to call it in the email.
In certain emails where I wanted the CMS block to show, I did this (Magento_Sales/email/order_new.html) - in a template (var/www/magento2/..../app/design/frontend/theme_name/Magento_Sales/email/order_new.html)- as an example:
{{block class="Magento\Cms\Block\Block" area='frontend' block_id="thank_you"}}
Hope this helps someone! :)