That sounds great, but could you please share some more details (possibly screenshots) with those of us who are less acquainted with the matter in hand? For me "rebuilding the column" does not tell much.
Not sure what “rebuilding” the column is, but if it is a short between E6 and VCC, then physically cutting the trace from the right column to the uC (mcu), then running a jumper wire from the column to the new pin (D0 in this case), would create a new path without a short. You would need to run QMK though, because it would allow you to change the pins used by the firmware (change E6 to D0).
You shouldn’t need to cut all the traces at each switch footprint and literally, physically rebuild the column (like run jumpers to/from each footprint like you were handwiring).
Though before I went cutting traces and soldering jumpers, I’d inspect the uC pins and pads, and the traces for the column that’s acting up and see if I could physically see any shorts or bad joints, and then clean them up/fix them, and see if that solves the problem. If there is a short between E6 and VCC, I would suspect solder bridging the gap between the pins/pads as the culprit, and cleaning up that area could solve the issue. (Assuming that’s what the problem actually is) and that would be a lot less damaging to the pcb than cutting and jumping traces (and also would allow you to still use the ymdk config tool).