The HTML Flash Viewer export file format is designed to work with the GraphMLViewer application, which supports links to external documents via context menu or single clicks on nodes. These links, however, don't seem to work when the exported HTML is opened by double click on the local file system.
Due to security reasons, Flash player runs its applications in so-called sandboxes. This should prevent a Flash application which is loaded from the web to access the local file system.
When started from the file system, i.e. by double click on the exported HTML file, the GraphMLViewer runs in a "local" sandbox: it is allowed to load files from the local file system but not to access the web. This is necessary to have access to the GraphML file to display. However, opening another web site is an access outside the local sandbox and thus considered as a security violation. For this reason, the GraphMLViewer refuses to navigate to another link when it was started from the file system.
It is possible to open links when GraphMLViewer was started from the file system, by marking the folder that the viewer is exported to, as trusted.
To do so, open the viewer, then open the context menu via right click and select "settings". Open the Privacy tab and click on "Advanced". On the settings page, which will open in a new browser window, select the "Global Security Settings Panel", select "Edit", then "Add", then select the folder that the viewer is exported to.
The Flash player settings page can also be reached by using this quick link.
Note that, when started from a web site, the links will work without further steps to be taken - see below.
Running GraphMLViewer from a website
When started from a website, the GraphMLViewer runs in the "network" sandbox. Hence, GraphMLViewer will open links to other websites without problems.