I'd say that your bridge has tilted.
If the nut is in place and the feet are in the same spot the only way to cahnge the string lengthis by moving the top of the bridge.
Get it up on the dining room table and check it carefully for tilt.
Also make sure the bridge is at 90 degrees to the centre seam/strings.
If all that checks out, move your reference marks. The harmonics ARE in the right place.
