Hi there
Of course, I'm not an Adobe developer, but I believe I may be able to offer up a clue on the files.
The process of generating an output such as WebHelp or Responsive HTML5 causes many processes to unfold. During these processes, the information that comprises the TOC, the Index, the Glossary, and the Full Text Search is analyzed and is broken into smaller and more easily served chunks of information. Generally speaking, each of those files contains a small segment of the TOC or the Index and suchlike.
I believe this helps make the overall project "speedier". For example, if your TOC has lots of nested levels, the top level items are loaded from those chunks first, then later the other levels are backfilled in the background.
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