We all know that if A Hero cause's someone's death or is responsible for a death or someone dies because of something they either did or didn't do that they lose all their Karma, as do all their allies

But then I had a thought, what if the hero isn't responsible for someone dying but he or believes that they are responsible for that person dying?, after all even Super Heroes make mistakes

Rules as written, it's all karma loss as an accidental death. Seems overly harsh in my opinion.

Also, only the hero seemingly responsible is the one to lose karma. The allies do not lose karma in the event of a death. If the case is mysterious then it's -50. But it's the death that matters.

If a person dies and they didn't choose to die, either by a noble sacrifice or a suicidal self-destruction then it's all karma gone for the one involved (or all if that's truly the case but very rare). If they didn't choose to die, but there's no body and the person should have died it's -50 to the group

But that doesn't answer the question of what if the hero thinks he or she's responsible but isn't, after all its not accidental death or mysterious death, he or she believes he or she was in some way responsible when in fact he or she wasn't in any way responsible for the death

My opinion is that if that happen then The GM should make a note of how much karma the hero lost and when he or she realizes that he or she wasn't in any way responsible for the death then he or she regains the karma that he or she lost

The most accurate way to emulate this is as you say- hero loses karma ( to mimic the guilt karma loss )

then gets it back later

I agree with the suggestion of removing the Karma then gifting it back once the truth is revealed.

I agree, hero loses karma as if death really occurred.

I would not return the Karma later just as I wouldn't return the karma if the victim was later resurrected. You could get into some really fuzzy situations if you retcon karma...."Remember when you thought you defeated Juggernaut? Really you didn't since because , so I'm going have to take that karma away now that you know the truth". or "Remember three weeks ago when you used mind control to convince your boss you weren't really on the schedule and I gave you karma for doing your job, well the mind control wore off, he realized what you did, and I now need to take some karma away." Too much bookkeeping and too much trying to keep things straight.

Also, remember that if the hero is the member of a karma pool, the karma pool also losses all its karma. See page 37 of the Advanced Player's Book:
"If a member of a Karma pool kills a character, or through his actions causes the death of another, both his individual Karma and that of the Karma pool to which he belongs is reduced to 0. (This is why the X-Men kept such an eye on Wolverine all these years.) Noble deaths, mysterious deaths, and self-destruction are handled as for individual characters."

yeah, that follows barna 10.

the emulation of the genre of superheros through rules mechanics is the way.

rule balance should take a side seat to this

I would never make retcon Karma a general thing. Killing someone should be a big deal for a superHERO, a defining event, so at the end of that B plot / quest / storyline I can live with a retcon Karma as a one-off thing. Effectively it's a much bigger than normal Karma award I guess which is another way one could describe it in more general terms:

"As well all know, retroactive continuity occurs often in comics. In game terms one of the only relevant effects might be when a previously dead character is discovered to have never died. This is different from a situation where a character, however unbelievably, has "returned from the dead." In the situation where a character believed to have died in fact never did truly die or suffer permanent debilitating injury, then if a hero character was believed to have been responsible, at the gamemaster's sole discretion that character may, when the truth is revealed, receive a special one-off Karma Award or Karma "adjustment" equal to the total Karma lost back when it was believed by all that the character caused the death."

I agree that retconning karma will lead to trouble. If the character believes they caused a death, then they should lose karma to reflect that (it's called karma for a reason). Similarly, if that character believes they're innocent, then no karma loss (Committing Crimes in the PH.

If it turns out the "victim" is actually alive later, then both player and judge have ample grist for the mill. You could even have a bit of fun with it. "Doctor Doom, I thought I killed you, but you were alive and in hiding this whole time? That cost me YEARS of therapy! Here's the bill, you sketchy scoundrel." The more litigious-minded could even sue the villain for pain and suffering along with material losses. Any way you handle it, it's great character development.