Well I was a Messiah when I started honest hearts. At the end of HH I decided that the dead horses and sorrows need to fight the white legs(but I let the leader live) so my question is does this action give negative karma?

I ask because today I reached level 50 and I saw that I had the "just lucky to be alive" perk available instead of thought you died. When I checked I saw I am a neutral dude and a true mortal now which I don't understand at all. After rentering the Mojave I didn't do much at all just did a meaningless legion quest which didnt have any killing and pickpocketed raul once but thats never cost me so much karma. After that I started up lonesome road immediately and at the end of that I persuaded ulyses to stop the bombs and didnt bomb ncr or the legion. Could that for some strange reason be the reason for karma loss? does any one know?

How strange. By what you explained you should have good karma. By sparing the leader of the white legs, I am fairly sure that I got some + karma.

By stoping the nukes from striking the NCR AND the Legion, now I do remember that that should be worth some major + karma.

Which Legion quest did you complete, if I had a name I should be able to help you out more, because I know that pickpocketing someone ONCE should not have done much damage to your karma standing.