When using the Import Font parameter to link another file, the alternate glyphs in this linked file will be overwritten by the host one. For example, 2.glyphs has Import Font = 1.glyphs, and there are a and a.2 in 1.glyphs. When trying to create another a in 2.glyphs, it will be forbidden. However, when trying a.2, it will just overwrite the original a.2 in 1.glyphs.
It seems it’s due to that a.2 has no unicode, but I think every glyphs in the linked file should be kept no matter if it has unicode or not.
These are the example files (you may need to change the path in Import Font):