This seems a rather new bug.
I've done this quest dozens of times, so I know the 'read all journals' - Stuff et.al, and never had any issues with it.
I did try again today, and all of a sudden... no more entry to the sewers. The quest tells the player to go there, but there is no questmarker and the sewers cannot be entered. (console works, so the sewers are still there)
I only use official Mods/creations and your patch of course. I disabled some of the newer paid creations, but it did not help.
This bug comes up since maybe 2 months now on reddit, so it seems to be rather new. At least it is new to me.