I'm using the grandchild plugin described on the page below. I want to edit the child themes footer so I placed the footer.php file in the /plugins/flannel-grandchild/templates/... folder but it's still using the child themes footer.php file rather than the footer.php file in the granchild plugin. Am I not doing this correctly?
While you can modify templates for pages, posts, and the like, I don't believe the header and footer files can be done in this way.
To be 100% sure, I am looking into this for you and will reply here as soon as I have some more info.
Unfortunately I was correct. Although there is a WordPress ticket that looks promising, the work is incomplete at this time.
Perhaps this will be possible with a future version of WordPress.