Harmy said:

Thanks Troy :-) It just bothered me every time I watched it, so I overcame my laziness and did it (the lightsabre work is terribly tedious and difficult).

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 have merged only mkv files, using mkvmerge and never had any problems with it, even the synchronization was always correct