Emilia has a horrible meaning, in my opinion, whereas I find the meaning of Amelia neutral. I would therefore choose Amelia. Amelia is also more common so has a bigger probability of being spelled correctly. I am not a fan of either, too common, but I really like Amalia.
Both names do have somewhat negative meanings, and Amelia can also refer to the congenital lack of limbs. These meanings are why I’d avoid Amelia / Emilia completely, tbh.