I beat the Kayran continued to play for about an hour, saved and quit. I came back a little while later and there were no saves after the Kayran fight, when I went to load.

I checked the save games directory and there are several autosaves and a quicksave all created after the autosave right before the Kayran fight, and none of them show up on the list.

I would rather not replay all that anyone else having a similar save issues?

I wondered quite often that there was no save file after I saved...

Then I found out that there are situation in which you cannot save. It says "You cannot save..." instead of "Game saved". And I just did not pay enough attention to notice that.

But in you case, you have files. Haven't encountered this, yet.