Was the issue with there only ever being one of certain skill books ever fixed?
I think that was changed. Using 'fixed' implies it was not deliberate to have unique skill books.
0 of our skills are lost.
Are you playing the console version? Maybe there is a difference between that and the latest PC version. I don't recall what version the game was at when I first tried respecing; I think it was a couple updates ago, though.