ok, figured it out - note to self: When fixing solder pads on a broken connector, fix all of them! And get new glasses!
The trigger signal is routed twice(!) from the Y-Board to the TB Board. Through pins 5 and 6 of the P2-3/1 connector. I'm not sure why this is done, but I suspect it enables the alternate triggering mode.
When fixing the broken connector P2-3/1, I had assumed the solder pad on pin 6 (on the right) was still ok, but on the photos you can see (in hindsight), that the connection to the trace is broken. Since I didn't want to remove the entire board again, I fixed it on the components' side. Not pretty, but I guess I'll get another chance to fix it for good at some later time.
Now everything is in working order and the Y-Out does output both channels 1 and 2.
As a side note, the pin numberings on the component layout schematic are wrong - 1 is 6 and 6 is 1 - in case anyone else runs into the same problem again.