I did a quick test on a bolt pretension load to see if that had any defect in the direction of motion of an adjustment load in 45 degree rotatated geometry compared with the original geometry and it behaved correctly in both cases.

Check that all bodies have the correct material assignment. I don't expect that would have changed.

If you can't find what changed, all you can do is start with a new Static Structural and rebuild the entire model with the rotated geometry and add a new Modal analysis to that new model.

Why did you need to rotate the geometry in the first place?  Is there an alternative where you don't rotate the geometry?