The way the HTML module works using IPortable (which creates and imports the content templates) the entire set of content is exported/imported as is. The only way you could account for this is to use a different structure when creating the links in the content. How exactly you do this varies based on which version of the Core you are using (5.2.2 in your case) as well as what URL Rewritting you are doing (likely stock core Friendly URL provider with human friendly turned on - which is default). This also depends on your navigation structure of the sites, which is likely to be identical based on what you said. So, if you are using stock DNN, you could essentially change you links to something like this:

www.domain.com/ParentPage/ChildPage.aspx. This would work if you had Parent Page in your top menu (Like we have Products, Development, Community, etc. on this site) and ChildPage would be the name of your target page. Generally I would recommend this type of thing but if you know this is going to be consistent across all portals and you are using a stock install it just might do the trick.