The bottom one is correct. To fix the top one: "If your father was alive, everything would be different."

"If your father had been alive, then everything would have been different." is grammatically correct. "If your father was alive" is grammatically incorrect but often used in casual speech. However, the usage would be "If your father was alive, then everything would be different". The correct grammar for the sentence would be "If your father were alive, then everything would be different".

If your father was alive, then everything would have been different.