I don't know the process you used for pre-bills but it sounds like somewhere along the line you posted the bills so that the items are already billed. If you go to reprint bills do you see the bills that were before the previous balance only? 

Sounds like you have some sort of filter excluding new items, try removing all filters just to see (print to display) if that lets them in.

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Yes, I see the bills that were before the previous balance only. 

Then you ran bills and finalized. When you run the second set they will only show balance forward because everything was already billed. You can reprint the first batch to send to the clients.