I selected all my letter glyphs and chose Make Component Glyphs, and it had unwanted consequences on some of them. My fault, I guess, but it would be a nice feature if Glyphs could skip replacing non-empty ligatures (both f_f, f_l, and all .liga) and ordinals, since those will seldom be comprised of actual default components in their final form.
I can’t change it right now as I can’t distinguish the case where you what to replace the existing glyph and when not. But I take note and see if I can find a solution.
You could create a smart filter for empty glyphs. And only apply the command to those.