I'm not sure if this works on every platform, but (in the Linux version at least) even though the text no longer appears selected, the search/replace module(?) seems to know where the text was selected.
You can click the "In selection" control (the right-most button just to the left of the "Find What:" box - the icon is a dark rectangle with a light centre) and the search/replace will occur only in the text that was selected when you invoked it.
Unfortunately, the text stays deselected after you perform this operation, so you have to select it again if you want to do another operation in that same text, so it's still not great.
I'm assuming this is a feature that the developers don't actually use themselves (or maybe they don't even use their own product to develop it?) or it would have been fixed long since.
This may be more recent functionality than the date of your post (I'm using build 3065).
