If this BOBW-SE release will be worldwide as stated before, i highly doubt they will cut it any other way than the existing movie cut, which has the deflector scene missing.
Otherwise they would have to alter every single dubbing track of the various languages to match, because they do either fit to the seperated episodes, or the movie with the missing sequence.
The existing movie version, from what I can see on Memory Alpha, was only released in PAL regions (and with the other 2-part episodes, aside from Chains Of Command
, only the ones originally
aired as feature-length movies have been released to the rest of the world), and more exactly just the UK. But considering what CBS has done with The Measure of A Man
, and even further back when Paramount released the season sets of Voyager and Enterprise and they used the UPN masters, which featured scenes not included in the international masters, I wouldn't be surprised if the feature version did include extra scene's---plus considering that Best Of Both Worlds
ranks up there with Measure of A Man
as some of the top episodes of the series---it wouldn't surprise me to see some scene extensions.