Omega 3.x base theme missing after Drupal upgrade
Where did you put your base theme?  

It should be in the same folder as your theme "sites/all/themes". If you put it in the top themes folder, beside Bartik, Seven, etc, it was in the wrong place and this folder is overwritten when you update.  

If his is the case you can probably just download it again and put it in the correct folder "sites/all/themes".