I did some more trial & error testing and I think I found a way. Here it is if someone is interested.
Add a value consisting of non-hex data in the third column in the GOADB, like uniX or NULL and FDK will leave the Unicode index empty for that glyph. And the best of all, no error is reported.
I also did a diff between two OT files; one using this "feature" and one not, and the only differens is the non-existent unicode values for that particular glyph.
/mårten