Too late now I know, and I think this may be why Ian was asking if it was glued up. Sometimes, a step can be caused by the locating pins on something like a fuselage, you know, the little pegs that fit into holes on the opposite side. Often these do not match up correctly and by cutting the pegs off, it is easier to 'manoeuvre' the two halves together by aligning the top (most visible) seam and using liquid cement, just work around the joint a couple of cm at a time. Often, this will allow you to get a step free joint or at least work the step to the underneath where you can be a bit more liberal with the sanding and less demanding of the re-scribing as it is not so much on view.
As it is already glued up, Ian has given the best advice I think. If the step is very bad then you could consider building up the lower side with ver thin plastic card and then sanding it to blend it in with the finished shape and the other side. Either way, I think you will have to re scribe any lines no matter what.