I'm pretty sure it will be an issue with all of them but you can select mutiple files in the Contents panel, right click and remove the layout in Properties there. It still won't be a quick job but it will be quicker. Obviously you only need to do that in projects you have to generate before we hear more.
You could also use any tool to find the topic layout line in the header section of the topics.
Adding the footer content to a snippet seems to work OK.
The snippet code would be something like this with the name of your footer.
<div data-conref="assets/snippets/Footer.hts"> </div>
and you could use a find of
</body>
with a replace of
<div data-conref="assets/snippets/Footer.hts"> </div></body>
That seemed to work but do back up first.
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My site www.grainge.org includes many free Authoring and RoboHelp resources that may be of help.
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