I wouldn't burn it unless you have a BD-RE disc, or have plenty of discs to waste. If it is out of sync on the hard drive, it will almost certainly be so on the disc.
I don't have a solution for you on this, since tsMuxeR is the primary free tool for creating Blu-ray structure, and its used in several other free tools. What format is the audio in right now? Is it DTS-MA or True-HD AC3?
As I said before, my attempts to combine Blu-ray movies worked well in tsMuxeR once I remembered to join them in that program.