Alright, so we were playing CE this afternoon and had a weird situation. The Red player attacked the Green player, green player used the Loser flare that made both players lose all involved ships to the warp leaving the planet completely empty. Next it was the Green Player's turn, he drew a green destiny card, the question is, can he attack his own empty planet to re-establish there a colony there? If we are interpreting the rules correctly, you cannot just establish a colony an empty planet, even your own. Perhaps we're wrong though. Any help would be great! Thanks!

This is discussed specifically on page 7 of the rule book in the left hand column.

If you draw your own color and have a planet with no ships at all on it you can automatically occupy it and it counts as a successful encounter.

"When drawing his or her own color, if a player has a home planet with no ships on it at all (enemy or otherwise), then he or she may aim the hyperspace gate at that planet to automatically re-establish a colony there with up to four ships from other colonies. Doing so counts as a successful encounter."

Page 7, If a Color is Drawn, Paragraph 3

Thanks guys! I found it in the rules almost immediately after I posted, of course, haha. Thanks again!