WARNING: The following contains spoilers for X Lives of Wolverine #2, now on sale from Marvel Comics.
Wolverine's long life makes him the ideal candidate for time-hopping adventures, allowing him the unique chance to protect Charles Xavier from a time-displaced assassination attempt. But the full repercussions of this mission haven't yet been fully confirmed, and could have a serious cost.
X Lives of Wolverine #2 (by Benjamin Percy, Joshua Cassara, Frank Martin, and VC's Cory Petit) pits Logan against an Omega Red-controlled version of his long-dead wife, Itsu. But considering how brutal their battle becomes, it might end up leading to the erasure of his son Daken from reality.
X Lives of Wolverine has tossed Logan across the course of his own life, forcing him to confront multiple threats he's faced over the years. Seemingly happening simultaneously across the time stream, Wolverine is forced to relive brutal fights from his youth and his time serving as a member of Team X, with the most tragic of these being his reunion with Itsu. Briefly Wolverine's wife after the events of World War II, Itsu remains one of the most important women in Logan's life. Notably, she's the mother of Daken, with her murder at the hands of the Winter Soldier and the subsequent framing of Logan for the crime being the primary reason the young mutant initially set himself up as his father's enemy. Logan gives in to the temptation to be with his wife again, only for her to transform into a deadly threat.
As Omega Red has previously shown, he is now capable of possessing anyone in the past and infusing them with his malice and powers. He does this to Itsu, quickly transforming her into a major threat. As Wolverine fights her, he remembers that he can't kill Itsu and rushes off to protect the history of Charles Xavier without risking the existence of his son Daken. Still unborn during this period, Logan has been warned about the consequences of his actions, but at the end of the issue Wolverine uses his claws against Itsu with seemingly fatal intent. While it would be surprising to see Daken retroactively erased from the time-stream (especially considering his prominent new role in Marauders), it is still interesting to consider the effects of Wolverine and Omega Red's battles throughout history.
Both men have been leaving a trail of bodies in their wake, with Jean Grey psionically offering Wolverine guidance that has largely gone unheeded. Logan has already thrown a man to his death in his teen years, and his decision to betray Team X instead of merely disappearing to complete his mission might place Xavier in danger. If Logan's actions do have an immediate effect on the time-stream (ala Back to the Future), then his actions might have cost him his son. Considering the impact Daken has had on the present day, that might also set off a series of dominos across the time-stream if his actions come with the repercussions the X-Men fear.
Even if that isn't the case, and Wolverine's interactions with the time-stream were always secretly a part of his life, his fight with his wife might have left her easy pickings for the Winter Soldier. In essence, his battles with Omega Red could have technically already happened and just been forgotten about due to the time-hopping nature of the battle. There's a question to be asked about how much impact Logan's actions are having on the time-stream, or how much of his life has secretly already been defined by this journey across space and time - and whether his son will survive the experience.