I think an amended form would be confusing in this case. An amended 1120-C is not a separate form. It has check boxes for initial return, amended return, etc. I would prepare an original 1120-C and submit it with a letter of explanation and request for the originally filed 1120-S be replaced by Form 1120-C.

You are talking about Form 1120-C for a cooperative association and not Form 1120 for a C corporation...correct? if this was a C corp, a late or invalid S election may qualify for relief if the election is filed within 24 months of its due date under Rev Proc 2003-43.

Also check if K-1(s) were issued & the loss was taken on the 1040(s).