Hi Rafster,
As far as I know this used to be a problem only with earlier iGuidance versions. Now you should be able to un-install and re-install with out loosing you favourites or maps. The un-install process will only remove the items on the Programs directory; it will however leave intact the "iNav iGuidance" folder in C\: (This folder contains your maps and also favorites.dat).
(Don't take my word for it. Back-up favorites.dat just in case... ;-)
P.S. The only reason I'm replying to you at all is your avatar