The GO has been reposted.
Seeing as all downtown service thru W4 on both 8 ave and 6 ave is on the respective express track, maybe it is for the W4 interlocking.
Also, the weird routings are probably because of the lack of switches to the Rutgers tunnel after W4.
Since 6 Ave still needs service, the can run normally
The therefore can run via 53rd st/8 Ave express/Cranberry to Jay St and normal over Culver
To avoid the all sharing one track, the can replace the via 63rd then run via Broadway to Whitehall.
Since the must run via 63rd/Bway in both directions, the uptown can go via 6 Ave local/53rd St to replace the (E). The side benefit being 57th/6 Ave is left clear for station work