Harmy said:

So anyway, before I start the encoding, can anyone tell me with certainty that if I encode each reel separately, I will then be able to join them (by whatever means) without recoding the video and keep the Blu-Ray compatibility and not lose any frames?

I'm not really sure but some time ago, I discovered several "timestamp problems" after merging two movie files. I don't even remember the format and doubt that both processes are comparable but since you're still waiting for hairy_hen's audio track and found out that the encoding error wasn't random I suggest not to take any further risks.