There are a number of possibilities:
First, Hans Fegelein, Hermann's father stated several times after the war that he received packages containing Bundesmarks with notes stating that Hermann was alive and otherwise fine, but had to remain underground. However, The money could have been sent to his father by Fegelein's long time comrade, Albert Faßbender who resumed his lucrative business with his step-father after the war as a chocolatier. The alternative is that Fegelein did in fact, survive the bunker. In order for this to have happened, he would have made a deal with Gestapo chief Müller. Müller and Fegelein also would have had to convince Rattenhuber, who Hitler sent to confirm the death of Fegelein, that he was in fact dead so the Hitler nuptials could take place without the possibility of Fegelein becomming a relative of Hitler by marriage. Fooling Rattenhuber by dressing up a battle death corpse in Fegelein's uniform was possible as there were so many corpses around the general area from the make-shift hospital on the upper floors of the Chancellory.
Next is the possibility that Fegelein was hanged in the Gestapo cellar as theorized by James P O'Donnell. In that case, his corpse would have remained in the Gestapo cellar until the Red Army investigated it in May, 1945. If he was hanged, his tunic would have been removed was the custom, so there would be nothing distinguishing him as Fegelein. Mohnke states that in the abortive courts martial hearing, Fegelein tore off his colar and/or shoulder pieces from his tunic anyway.
Finally, there is the possibility that as reported by Hanna Reitsch, Fegelein was shot in the Ehrenhof. His body would have been hastily burried and removed to a mass grave later. I once saw a Soviet Newsreel that identifed some of the corpses that they recovered, but Fegelein was not among them. I also read an account somewhere, and I am sorry that I do not remember the site, that a Red Army private recently came forward and claimed to have burried him in the top level of the chancellory. Again, to fool Rattenhuber, all they needed to do was dress a corpse in Fegelein's tunic and shoot up the face. at 11:45 PM April 28, 1945, I doubt Rattenhuber's powers of observation were anywhere near 100 per cent. Also, due to Red Army shelling, he might not have had regular sleep for going on several weeks.
Mohnke states in his interview with O'Donnell that Fegelein was in uniform during his abortive courts martial hearing. The mufti would have been brought to the bunker as evidence of his intent to desert.
The reason for the execution was that Hiter learned of the negotiations of Himmler with Count Bernadotte circa 9:30 PM on that Saturday evening.
I hope that this does not add to the confusion.