Hello and welcome to our forum!
This problem should not happen. When you added the new fields InfoPath is supposed to automatically add in code to "upgrade" your old instance documents to add in the new fields. Something must have gone wrong there.
The only thing I can suggest trying is:
1) remove the 2 new fields.
2) save and publish the template
3) add back in the 2 new fields in exactly the same place and namign as before.
4) save and publish the template.
5) then try to open your old and new files.
Be sure to backup each version of the template along the way as well as your data files just in case something goes wrong.
If that doesn't work what you'll end up having to do is manually open each of your existing files in notepad and manually adding in the missing nodes into the XML. You can figure it out by comparing an old doc with a new one. If it's less than 100 files sometimes that's faster than trying to figure out what went wrong. :)
I hope that helps.
Shiraz Cupala / Microsoft InfoPath MVPQdabra® Software / Streamline data gathering to turn process into knowledge