Only the temporary test encoder was given 24V (directly, not via the 7i48) and then only briefly, so fingers crossed I haven't killed it.
The 3 encoders I need to use are the split output from 3x Yaskawa servopack, so physical encoder on back of servo is connected to the servopack, which provides a, /a, b, /b, c, /c outputs ("Divided encoder signals are output"). Unplugged from the 7i48, these are visible on an oscilloscope.
The single ended/differential jumpers were correctly set.
I watched encoder.01.position, encoder.01.rawcounts, and encoder.01.counts (iirc) while the Y axis was moving and Y encoder was wired in to the 7i48; all encoder counters remain at 0.
The one thing that stands out to me on the wiring side is that there's no route for the +5V encoder supply from the 7i48, to go into the servopack. However per the attached diagram (screenshot from the servopack manual), no +5V line is shown.