Which of the two y's is easier to lose?
heard as hypogimnia
spelled hypogymnia
The second, which is how hypogimnia happens. It is hypogymnia, from gymnos.
What the ear did
By the time a listener reaches the third syllable they have already spent effort on the first, and gim is exactly what that syllable sounds like. English keeps the y in every relative of the word, from gymnast to gymnosperm.
H-Y-P-O-G-Y-M-N-I-A
The full entry for hypogymnia covers the name itself.