It's been a while since I played Suikoden I, but here's my theory ^.^...
I may be misunderstanding this topic, but I think it seems it was originally about the whereabouts of the Front Gate Rune and Sovereign Rune along with their carriers Windy and Barbarossa following the Gate Rune War.
Nearring the end of Suikoden, after the battle against the Golden Hydra, Windy confessed her betrayals to Barbarossa, taking her ressemblance of Claudia as her advantage along with her Conqueror Rune. In response he confessed that his Sovereign Rune had protected him from the magic and saw her through her actions through compassion for her. In reaction she begins to refuse Barbarossa's confession, but he embrace's her and jumps off the Floating Gardens with her in his arms.
In my opinion I believe that there was a certain adorning Windy had for the emporer and later realized what she had done to him after the confession, trying to deny feelings for him in the end. And my possible theories start after that incident...[/spoiler]
Theory 1: Both Windy and Barbarossa Die
After reading the information in the article "True Runes" in the "History" section of the site, I noticed that it mentioned a True Rune Bearer's immortality only came from a halting of their aging, and that they could still die from physical injury. Since they did infacted jump off the gardens, this theory simply inquires that they did die among impact... however, that doesn't explain missing boddies ^^;;
Theory 2: Windy and Barbarossa Live on Together
The ending for the Suikoden I in my opinion seemed to put Barbarossa and Windy in a suttle relationship. After their jumping they could have survived since they both should have some endurance being granted effect from bearing True Runes... Having lived they could have reconciled and ran away from Toran, Barbarossa giving up what little he had left in exchange to live his life in happiness with Windy... which would explain the missing bodies, but might not be very believable to those of whom don't think they had a relationship or anything of the sorts.
Theory 3: Barbarossa Dies and Windy Lives on in Hiding
Barbarossa mentioned that the Sovereign Rune was imbedded in his sword, not his body. Referring to an example between Viktor and the Zodiac Sword (Star Dragon Sword) there is no proof that he was immortal. It really can't be assumed that Barbarossa was immortal, because there is no proof Viktor was when he had the Zodiac Sword (Which supposedly has the Night Rune imbedded into it or said theory). If Edge during Suikoden III had further explained his encounter with Viktor, maybe mentioning his appearance or Viktor actually telling him he had immortality, then it could be assumed that a true rune doesn't need to be attached to a body to grant effects. Concluding that when Barbarossa fell, he possibly didn't have the strength of the Sovereign Rune and died on impact...
Moving on with the theory, Windy however had the Front Gate Rune on her body and even with only half a True Rune she obviously had immortality or prolongued life, being well over 300 years old(300 years ago, she destroyed Ted's Villiage). With the strength of the rune, she could have possibly been able to survive the fall given the rune's effect on her body's endurance. Feeling sympathy (See romance inquiry in Theory 2) she carried Barbarossa's body away and could have burried him somewhere secluded as to keep his grave away from those of whom now despised him as the Vile Emporer of the Scarlet Moon. She then could have taken the Sovereign Rune and accomplished her goal of 2 True Runes or she could have burried it along with Barbarossa. Nevertheless, she still would have had to go into hiding because Harmonia was once after her rune, why not go after it again?
And those are my theories as to what could have happened to the Front Gate Rune, the Sovereign Rune, and their bearers. I'm still new to the Forum thingy but this seems fun <(^.^)>