As far as I know, updating the icons in a Windows EXE or DLL is a perfectly fine thing to do. This includes enlarging icons, adding extras, etc.
I use MicroAngelo for editing icon resources directly in EXE files, and I have never had a problem when I'm simply modifying or adding to the resource table. The editing software simply handles updating all of the necessary references in the file.
The only time I could see this being a problem is if the EXE did a self-checksum as part of a copy protection scheme. But I haven't seen a case of this before, this is only a theoretical idea.
In fact, I've gotten to the point where I'm so confident when editing icon resources that I don't even bother to make a backup copy of the DLL or EXE that I'm editing. I just save directly to it and get on with my life.
Related question, I'll throw it out to the BBS:
Back in the old 16-bit days, I used Borland's "Resource Workshop" from their IDE to edit resources directly in the EXE files. Not only could you edit icons, but you could also edit menus, bitmaps, and dialog boxes directly in the EXE. This allowed for nifty things, such as re-arranging the menu of a program to suit your tastes, or fixing the tab order of a poorly-written dialog box.
This program doesn't work on newer 32-bit EXEs. Is there an equivalent tool available for newer software now?
(Edit: /me goes looking for this "Resource Hacker" program mentioned in the original post)