I think you can leave both contacts on. Just overlap the shape exactly and it’ll only recognize it as a single contact/diffusion. Should pass DRC that way. If not, once you overlap it, remove the contact of one of the devices. If you overlap shapes in layout, it just looks at the total area of the shapes, not the various layers of that shape. Once everything is done, its essentially flattening all your shapes. Also, as long as you meet DRC rules, diffusion shape outside active+gate doesn’t matter. You can create a dogbone diffusion if you need to add more contacts so you don’t have lonely via violations.