I feel like I’m missing some tiny detail here, but I want to save a UFO file as a .glyphs file. (because it now has multiple masters, etc.) How do I do that?
Open the UFO, choose Save as… from the File menu. Does this not work for you?
A single .ufo cannot contain more than one master. Perhaps it already is a .glyphs file?
What version of Glyphs and Mac OS do you have.
Depending of the version, you might need to Duplicate it first and then you can Save As… Or, if you have the none App Store version, you can disable the “new” saving behavior in the preferences.