Hi @seank, I am not exactly sure what you are trying to accomplish, but if you open the exported file, which is using relative paths, and update that link after import to dreamweaver (or whatever tool you want to use), and point to index.html instead of "/#", I am thinking that may solve the issue in the short term.
As far as why this is changed by that program when imported to another took, I cannot say. We produce standard html5 pages using a relative path structure.
We export the .html extension automatically for all pages.
I would suggest to create a step by step list, how you are getting from the export file that works, to the state where it does not work, and check each step of that process