The only things that can affect the camera alignment are:
- physical movement of the camera or bed
- changing the focus height of the bed (different lens, adjusting lens tube height, etc)
- the Shift / Width / Height controls in the camera control window
- Running in User origin or Current position instead of Absolute Coords
The first item, the camera being moved, is probably the most common. If you bump the mount and change the angle of the camera even by a degree or two, it’s not likely to be visible to you, but changing the direction that much will affect the alignment a lot.
You shouldn’t have to redo the lens calibration, only the alignment.
Since you said it’s only off on the Y axis, that suggests the lid not opening to the same position, because that wouldn’t affect X, just Y. If you have a camera mount with a hinge along Y, like ours, that would be another possibility.
Any of these seem like the culprit?