They might take a temporary hit, but it should sort itself out in a couple week, and yes - greatly IMPROVE things.
And that temp hit is a worst-case scenario. Really. It'd be the same with switching to any other themes. Tho chancing themes should not affect linking within your own posts.
These forums were CLOSED to new posts on November 19th, 2012. New forums are here: http://www.studiopress.com/forums/
and you will need to SIGN UP AGAIN.
If you need assitance with setting up your theme, go to http://my.studiopress.com/
and read the SETUP links or the TUTORIALS link on the side tab.
If you need Account Assistance
, file a help desk ticket at the same location.