Originally Posted by kiwidude
When you hit the Step 2 match screen, it will show some books already exist (from your first file). At this point you use the Update Metadata feature, and tick only the MyRating2 column to be updated for those selected books. All the other books (which are new that you have created empty books for) should have values automatically set for MyRating2.
Even if you did put both MyRating1 and MyRating2 in your same configuration, then it should still work, provided on the Update metadata screen for the selected rows you make sure to only tick the MyRating2 column.
My problem boiled down to being unable to find the option to select the matched books - then I decided to try a right-click and found it!