but then the entire body of the people of Israel remained in that country; wherefore there are but two tribes in Asia and Europe subject to the Romans, while the ten tribes are beyond Euphrates till now, and are an immense multitude, and not to be estimated by numbers.
You can see here the entire quote in the works of Josephus Antiquities, Book XI, Chapter V, Paragraph 2.
An immense number to me would indicate more than an area in complete ruins....and deserted. Remember, Babylon was also considered a territory as well as a city. Many Jews did not return (600 B.C.) with Ezra and Nehemiah. This was where the majority of the "Talmud" was developed. See Talmud
Well, no, Babylon was not deserted; of course not. The empire was destroyed, though. I've read Josephus before.
But, to take Scripture as our guide, one must go to Revelation to find out what Babylon actually is. Babylon is a city built on seven hills. There is only one ancient city that is rather famously known as the city on seven hills: Rome. Babylon certainly wasn't.