The board cutout is on the "multi-layer" layer. It's drawn like other polygon cutouts with a dashed perimeter line that is the same color as your multi-layer color. As long as you have the multi-layer layer on, you should be able to click in the middle of the board cutout to select it. If the object select list pops up (due to multiple objects intersecting the area you clicked), it should be in the list as a PolyRegion with the description of "Board Cutout". Once you have it selected, you can modify or delete it as necessary. In your case, you'll probably just want to delete it and create a new one (using the same method you used previously). Or you can use the modify outline vertices option for the existing cutout, but that can be tricky.
Hopefully that is clear. Good luck.