I am not entirely sure I understand the plan, but it sounds like you have linked text boxes throughout your document of which you occasionally have a reversed page for the start of 'chapter'?
If you know how many pages you have in each chapter you can always use http://www.mymacmac.com/InDemand/InDemand.html which you don't need to link the text boxes on each page, as long as there are not more than 20 paragraphs per section. Or just collect the text into files as pages/chapters and have indemand place those.
If you just use indesign you could try XML tagging as Chapter page1 for each chapter but that will require you to tag each chapter page 1 manually.
Have not had a lot of experience with XML sorry.