1. If you had to re-install Windows. you have to re-install all of your applications, and additionally re-register anything like Dimension Pro and Sonar.
2. Any data you loaded onto a secondary disc should not need to be installed again, just the programs that use the data.
3. You have to give us information on how your soft-synths are setup in the project, as well as their corresponding audio tracks, and both audio and midi ins and outs.
4. Additionally, please detail your audio interface Sample Rate, ASIO Buffer Size, Recording Mode in Sonar, and detail all plugins present in the project.
Nobody can assist you until we know how this proejct is setup.
Bob Bone