There is no real merging but there is no real pause between the two e sounds either. As a native speaker, I can hear both e's clearly but it is a lot clearer with headphones rather than laptop speakers. It really makes a difference (even) in my case! On the speakers I hear a long 'e' while there would be a just a short one if there was merging. In short: your ears work just fine! :)
See here for more information on vowel merging. In the example above it would become "Αυτοί 'ναι άντρες" (aphaeresis) and the result would be a short 'e' sound.
Thank you for all that useful information. I would have thought my bluetooth Bose speakers would enable me to hear the subtleties, but you are right, earphones are better. And I need to 'get my ear in' to spoken Greek, to which end I think duolingo will help enormously. I am new to it and most impressed. Thanks again.
Αυτοί is the plural for masculine (the plural for he, if that existed in English) and αυτά is the plural for neuter nouns.
So, let's say we have ο άντρας (masculine noun): Αυτός είναι άντρας=He is a man, Αυτοί είναι άντρες=They are men.
If we have το ποτήρι (neuter noun): Αυτό είναι ένα ποτήρι=This is a glass, Αυτά είναι ποτήρια=They are glasses. ;)