Harmy said:
And can you make sure that it doesn't recode your content?
Yes, provided it's BD legal (at least, according to Adobe's definitions!)
edit: I just did a quick test using your latest encode. Encore hangs (indeed, locks up my PC entirely) when trying to use either the m2ts or the demuxed .264. Bummer.
I don't know much about x264 other that its Handbrake implementation - is closing the GOPs for a new encode an easy (and non-destructive) option as Chewie suggests?