I think I shared a map of a new connection between Jay St on the tracks to the outer tracks at Hoyt-Schmerhorn Sts a while back.
I had a couple of ideas and one of the things I had to settle on was an at-grade junction for southbound trains coming from Jay St seeing as that area is already complicated enough. Unless there was a connection to the old Court St station that allowed for service to return there, I highly doubt this would be an issue.
Unfortunately, from what I remember hearing this from a TO, the connection isn't possible on Jay St side of things. Something about the lack of bellmouths if I'm not mistaken which would've been very helpful had it been there and less service disruptive. Though, to be fair, the 63 St connector had to widen QBL to allow for both lines to connect.