Worried about the BackDoor.Flashback.39 trojan? Apparently, so is Apple. OS X Lion users that fire up Software Update will find a suprise — a second Java patch in two days. Whereas we previously might get a couple in a year, the rapid spread of the BackDoor.FlashBack.39 trojan has resulted in the mother of all Mac botnets with 600,000 enslaved Apple badged computers, including hundreds in Cupertino, too, which has our favorite fruit company scrambling to contain the damage.

Apple has now posted an updated Knowledge Base for this update: Java for OS X Lion 2012-002, which “delivers improved reliability, security, and compatibility for Java SE 6.”

Though Java for OS X Lion 2012-002 appeared in Software Update late Thursday, Apple’s Support Downloads page doesn’t yet list it. Further, the links provided in Software Update direct the user to Wednesday’s Java for OS X Lion 2012-001 Update and related security content Knowledge Base articles.

So, it isn’t clear what has changed in Java for OS X Lion 2012-002. It’s worth noting, however, that Apple hasn’t updated the Snow Leopard version of this Java patch.

Are you infected?

If you are concerned that your Mac may have been compromised and taken over, the Fairer Platform has published an easy to follow diagnostic how to — you will know in moments whether or not your are affected.

From the “for what it’s worth” department — Apple updated OS X’ embedded trojan blocker, XProtect, definition list on Monday, April 2. This integrated security measure, when properly up-to-date, can block trojans from infecting your Mac and can remove an existing infection.

Both the updates and protection are 100 percent automate, and the only way to know if Apple’s on the stick or not is to check. An easy way to do that is to download and run Adam Christianson’s Safe Download Version, which is free.

Apple updated XProtect definitions on Monday