Sorry; I got confused about the length of the program. For the record, there are times where a do-over is what is easiest. Menus (the psd structure) is not usually the problem, and can be reimported. But chapter markers (if you did not export in a form that brings them in), navigation etc. can take time. But it is faster the second time through.
Please post a screenshot of the settings you are using to transcode.