The screen going black was intentional, it was when it intercut with the events where they cut Naomi out of the tree, no other way of doing it sadly. It also happens later when Ben and Juliet are discussing her infiltration into the survivors camp.
Not the first time it was brought up, there was an explanation for that, even on the original site. The way I see that “mind-travel” is that it’s happening inside his head as opposed to actually going back (like in The Constant), but also from a technical side, it would be tough to edit it in cause it shows glimpses of the island events (which would be odd to see if we didn’t see them already), and for Charlie when the rain hits is completely different between that and his flashback (where Desmond isn’t there and he then saves Nadia from muggers). So I left it as is for this remaster.