So I am assuming that you have an add on to os-commerce that exports all of your product urls into a tool that formats a feed to Froogle. Not sure how you would go about changing the tool to pull the re-written urls that without talking to the people at os-commerce.
This is an issue with the data you are supplying to froogle, not with froogle itself. The code that generates the export file needs modifying - as mentioned, this is an osCommerce contribution issue.