Some general tips to try in any order you want:
1) Remove all content except for your eyes, clear cache and start game up, see if they are working.
1.a) If not try downloading a different lot of default eye replacements & see if that works. If the new set isn't working try downloading a new mod folder & see if that works. The next 2 suggestions are to do as a last resort) You may have to remove the sims 3 folder from my documents & start the game to force it to create a new folder. Or worst case scenario reinstall the game.
1.b) If they do work you'll have to start working through your cc to see what may be causing a problem.
2) Make certain you haven't accidentally deleted them, things happen when you are messing with stuff.
3) Try moving the default eyes to the override folder, this will give them higher priority within the game to be used.
4) You should just need to delete simCompositorCache and within the world cache folder anything that looks like this: worldname_sims, (you can delete the object one as well if you want.) regarding sim textures.
5) I've noticed recently that the Sunset Valley, all expansion packs incl vacation, university, future worlds, npc & townies will not automatically use default cc
Your sims, store worlds & cc worlds should be fine. You'll either by using NRAAS or cheating take them into CAS, edit them in some way & go back into the game to get the defaults working. If the default eyes are not showing in CAS, the game is not recognizing/using them for some reason.