Also, I'm not sure what resolution you did those scans at, but if you're rescanning them anyway, I strongly recommend scanning at 600DPI resolution. Basically you never want to have to scale anything up when making covers (since the quality will be lower than if it was high enough resolution to begin with), and especially when adapting to a different type of case - like from a Japanese GBA box to a DS case - you're bound to do some resizing and fiddling around, so it really helps if you have bigger margins to work with. Plus, higher resolution makes it easier to get rid of dust, scratches and other imperfections.
When you submit new scans, just use the same filenames and they will overwrite the old ones.
