I was looking in the BGB, under Universal Special Rules, when my eyes came upon the second paragraph.

It reads, 'The Special Rules marked with an asterisk (*) are automatically lost by an independent character joining a unit that does have the same special rule.'

These are the ones marked: Counter-Attack, Fleet, Hit & Run, Infiltrate, Scouts, and Turbo-boosters.

My question is since there is no specific writing that the Autarch gains the exarch's power the Autarch and the squad would lost the said ability. Therefore Hit & Run would be nullified if an Autarch joined Warp Spiders...and Counter-Attack would be nullified if an Autarch joined Howling Banshees...

So am I correct with this assumption or is there some hidden writing in the Eldar Codex that I have missed about the Autarch.

Kaanaelis

Your assumption would likely be correct, however there is a small paragraph that states that Autarchs can make use of Exarchs powers if he joins the squad, but no other independant characters such as the Farseer. I'm not sure as to the exact wording of this however, so you might want to double check.

I think the phrase is in that small bit between the unit descriptions and the actual army list.