On my 2007 Eos, I have had the left side metal clip that latches the cover onto the pins on either side of the trunk when in the cover is in the lower position come out. When the metal clip is out the cover does not depress a micro switch that is used to sense the cover being down. As a result the Top will not go down. I have been able to push the metal clip back into place with some friendly persuasion, but it popped out for the fourth time last weekend. May try something more drastic next time it pops out like using a little adhesive to help hold it in.
If you have found a U shaped piece of metal on the floor of your trunk about 1" long by 3/4" wide this may be your problem! Good luck.
If you have found a U shaped piece of metal on the floor of your trunk about 1" long by 3/4" wide this may be your problem! Good luck.