That sounds pretty much the same thing I have been doing. I have implemented each topic shown on the contents page as an individual subfolder. Each of these subfolders contains html pages of a single topic. I had the same problem with creating links to join different pages and creating links back to contents page. So I made a solution I described earlier where there is no need to create static links to the contents page or to any other page. You just put expressions like %NEXT_PAGE% or %CONTENTS_PAGE% in you html files, and then create a simple xml file where the order of the files and the subfolder hierarchy is described. After this the module reads the xml file and replaces the expressions with correct urls.
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