Hej Steen!

The problem is that what EA generates isn't really HTML but a completely proprietary, and completely undocumented, mass of JavaScript. This means that as soon as you try to go outside the intended use, ie what the designers envisaged back when the function was first implemented, you hit a brick wall. And what the designers envisaged is a single generation from a single root node of a single project.
But there might be a way forward: query URLs.
The generated HTML will serve query URLs, including
?goto=1:1 and
?guid={xxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx} (the latter allows you to link to either an element's or a diagram's GUID). So in one diagram you can add a hyperlink diagram object targetting the HTML version of another diagram, provided you know the directory on the server where the relevant
index.html is located.
Since the query link targets the GUID it will survive re-generations (provided the target diagram isn't deleted, obviously). However, any type of diagram reference created by dragging one diagram onto another (diagram frame, diagram reference, diagram hyperlink or navigation cell)
won't work since the generated URLs for those all target the HTML file under the assumption that everything is part of the same generated HTML.
But if the number of cross-generation links is reasonably low, and you don't mind the hyperlink diagram objects in your diagrams, you can link between different HTML generations using GUID-query hyperlinks.
If you need larger numbers of cross-generation links, or if you need a more dynamic solution, it might be possible to achieve that with query URLs in conjunction with a customized HTML generation template and/or some stereotypes and/or some scripts.
HTH,
/Uffe