There is no way to automate the process. You could do a move transform to move the whole glyph up, but not just one contour.
Anyway, you will need to manually edit each glyph to remove those red warnings, they probably indicate intersecting contours. In the Pro Edition, the Validation wizard will remove some errors, but not those.
Modifying the transform script to make the outline lighter may reduce the number of such errors.
See this thread: How Long Does it Take to Make a Font?