I created a f_i ligature and decomposed the components (both of which existed) and yet I get a “Empty Base Glyph” message. I can’t understand why this is happening especially since the outlines are clearly present in the glyph window. Anyone?
These empty components are in the background layer of your f_i.
Press Cmd + B to access it and delete them.
Can you select them by hitting Cmd + A repeatedly?
Janus: I tried your suggestion, but there doesn’t appear to be anything to select. There is nothing on the background layer from what I can tell.
It looks like you have one of the other layers visible (the 
icon in the Layers palette).
Yes, thank you! It was the bold version of the font. I deleted everything from that layer and the message is gone. Still a bit confused as to why it appeared in the first place because there was no “empty base glyph”. Regardless, it worked!
when you add a glyph like “f_i”, Glyphs adds component for “f” and “i” as a base to get you started. But if the “f” or “i” doesn’t have any shapes, you should see anything and wouldn’t know that the components were there. So it shows this placeholder.
Thanks, Georg! It’s strange because those glyphs did exist. It may have pulled idotless instead of “i”. Not sure where I went wrong, ha!