There is a function to convert any path selected to a cut contour as Flexi recognize it. I think it's in the menu "Objects", named "Cutcontour" with submenus to convert and release. So just select your Contour and convert it.
Close. The function to which you refer is Arrange->Contour->Make Contour Cut | Release Contour Cut
To import a contour line from AI make the contour cut a solid filled object, generally in some landmark color or another, with no stroke. Import the file into Flexi, select the object, and do Arrange->Contour->Make Contour Cut. At this time Flexi will convert the selected object, the solid fill will disappear and a [usually] gray wire frame path will appear in its place. It doesn't matter where the object is in the stack of objects; top, bottom or somewhere in between. In fact, it's easiest if the contour cut object is on top covering everything else. It's easier to find that way. Just select it, make it a contour cut, and, as if by magic, everything under the contour cut object in the object stack will reappear.