If you have a race with scored and uncored racers competing at the same time, would there be two seperate race codes and seperate paperwork such as referee reports, etc.

I can't answer your question, because I didn't know you could even do that.

If it is allowed in the rules you'll have to change the race code to produce different results since there's only one place to enter it.

This seems like a situation where the new 'hide / expose' feature could be handy (I love this feature by the way!). You could hide any competitors you didn't want to appear in a particular report and then expose them when done.
Note that if competitors are 'hidden' and you go into timing, the system still won't know about them!

Dan, the RACE itself... is either a scored or non-scored race. some of the competirors may not care about the scoring... but the results go to USSA... and they collect all that stuff. The racers may not have any scores (points), yet, but entering the scored race will give them some. These are j1s & 2s we are talking about - right ?