Hi Sean,
I agree with Wayne that it's probably better to have a good local luthier (like David's associate Jeff) do the work. If you've got inlays, the very best thing would be to replace the fingerboard, as sliding over different materials produces different sounds.
I've seen plenty of times where folks will inlay ghost frets on a board and leave the original inlays. It doesn't bother everyone, but I think it's more likely to bother an Alembic player since the sound is so clear to begin with.
FYI it's $550 to replace the fingerboard. You can elect to have unlined, lined, or sidelines. If things go well, we'll need it for about 2-3 weeks. If it turns out to need some finish work, it's another month on that.