Personally I think it starts either immediately after III ended, or right on the start of disc 4 and they'll be remaking the entire ending into the beginning.
I mean, if disc 4 was actually a sort of epilogue and originally meant to be the start of Shenmue III, this makes a lot of sense.
Also as strange as it may sound, I hope everything about it stays the same. Yes, give me that glorious floating, glowing sword in the beautiful Guilin caves in full HD.
And if you'll notice, the kickstarter video is a proto of the beginning of disc 4 as well... so yeah!