From what I've observed (I wasn't in the area at the time), just west of where the DL&W crosses above the Erie west of the tunnel portals, at West End Interlocking the Boonton Line swings (compass) northwesterly and descends to parallel the Erie Main Line (except for the NY&GL) for some distance. In that area they put in parallel crossovers to the Erie tracks and named the interlocking Bergen Jct. A new single connecting track was put in, descending from just east of the bridge over the NY&GL and descending to join that line.
All this left the Northern Branch out in. the cold, requiring trains from Hoboken to proceed beyond Bergen Jct., then reverse via the Erie toward Jersey City to a point where they could then move west onto the branch; that service was soon discontinued. I'm not sure whether the NYS&W was still operating to Jersey City at that time or had already pulled back to Susquehanna Transfer.
(Of course, today the NJT Main Line stays on the old Boonton Line at Bergen Jct., while the present Boonton Line takes the old NY&GL, and the Bergen County and Pascack Valley--the line formerly known as the NJ&NY--take the old Erie. But that's another story, and a long one.)