If the original file was created in Photoshop, the only type of file that can be exported from it is a jpeg type file. Just by exporting to an Eps file, doesn't give you the vector lines you need to add the contour cut lines.
If it was vector artwork to start with, your customer may be able to export it to an EPS from Illustrator. You would then need to > ungroup the artwork in Flexi and then unmask it. If your able to unmask it, you would delete the black box it creates. You may have to do this step multiple times until you can see all the artwork.
If you can't get to the Vector artwork, then your only choice is to draw a line around the area that you want the cutline. Assign the cutline, and once it's printed and cut, you weed out the white box.
Last idea, send the file to a service such as Vector Dr. or others and have them vectorize it. If the file has pictures or gradients in it and you have to print that paticular file, you can take the vector cut lines you need from the vectorized file and overlay the cut lines on top of the original file in Flexi. Export the file from Flexi with the new contour cut lines as an EPS file and print and cut.