After the Crisis Karen felt devastated: In addition to be the last survivor of Krypton, her home dimension had been destroyed and her family, friends and teammates were dead. If it were not enough, she was told that she was not Kryptonian or Superman's cousin. She feels so crushed, thinking that her life was a lie, than she feels even worse when Ma Kent tries to cheer her up.
Karen and Kara never made up, after their falling out due to the incident in Kandor, before the DC Universe rebooted into the New 52. Post-Convergence hasn't revealed anything about it yet.