How to Align Spectra (and How Not To)
If you have tried to align the overlay with the main spectrum by changing the “horizontal offset”, you are in good company, but you are wrong.
The purpose of the offset is to create stacked plots; for example, to show the main spectrum in the left half of the page and the other spectrum in the right half. For this reason, the amount of the offset is measured in screen points, a unit that has no fixed relationship with the experimental points.
Nothing stops you from misusing the offset. You could use it to momentarily align the peaks of two different experiments. This is conceptually wrong and a sure cause of trouble. As soon as you change the zoom factor, you lose the alignment.
If you need to align two experiments, adjust the chemical shift reference of one of them.