In this case you are using form-based email workflow. There isn't a codeless way to automatically save the file to a shared location and then send the next recipient just a pointer to that file.
The reason why InfoPath asks to save the file after that submit is that is to be sure the user is notified that they haven't saved their own copy of the form.
Essentially, you should ignore the save version and only be working with the version sent around in email. Your HR person needs to be the last person on the email workflow chain to get that final copy.
If you have SharePoint you could save the file there but still the email from InfoPath will send a copy of the file.
In Office SharePoint 2007 they provide out=of-the-box workflows for exactly what you're trying to do (routing, email notification, etc). That would solve your problem without having to write code, but of course you'd have to buy that product.
Again, you could write code to work around the issue partially, but it still requires telling InfoPath where you saved the file before sending the email so the email can contain that path.
Shiraz Cupala / Microsoft InfoPath MVPQdabra® Software / Streamline data gathering to turn process into knowledge