While working on a color font, I’ve run into a few issues in the color layer panel:
Glyphs crashes when selecting another color layer while the color-dropdown (in the panel) is open.
Drag and dropping the layer order makes the fallback glyph disappear. This happens in all masters (also non-color versions).
Another note: In Glyphs 2 it was possible to rename your color layer manually by double-clicking, is that option removed now? (I found it usable for creating alternative/past versions)
If you set the file format to ‘Glyphs 2’ in font info > other, you should be able to open it (if it lets you save in that format). If you saved in G2 format and it doesn’t open there, can you send me the file?