The three files restored (because it would seem that there were other edits made to try to get this same thing to work in a different manner needed to be undone), were from the Responsive Sheffield Blue (RSB) version 2.0 fileset that can be downloaded from the responsive templates area of the ZC plugins.
With regards to the section IDs, if you open each of those three files, you will see towards the top that there is an html tag beginning with <section... If you take note of the code that was provided
at the related post, you will see that specials lined up with section-3, featured lined up with section-2 and whats new lined up with section-1. Well, what is shown there is the "original code" from the tpl_index_default.php file. If you look at each of the three files, the section ids in the same "file order" are: 3, 1, 2. (instead of 3, 2, 1 as shown in the tpl_index_default.php file)
Therefore, to have the information line up together, it appears that they modified the section information in 2 of the 3 individual template files so that basically tpl_modules_featured_products.php had <section id="section-1"> and tpl_modules_whats_new.php had <section id="section-2">.
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