If you use the "Publish Files" in the Merchandising, Custom Templates Include section to keep your CSS and JS files, you have to do a total regenerate to get any changes to these pages made available to your store pages. We have thousands of pages, and products so this takes awhile.
We currently load a standard page edit and then just save the file to trigger a "Publish" sequence.
Please Make it possible to Publish the changes to the "Publish Files".
MarkB