If it were not for em-dash, we would no doubt keep the subordinating comma:
"It was only to be expected that Troy should fall — and fall emphatically, its very location effaced and, for millennia, forgotten —, because the Gods and heroes on the Greek side were among the most powerful in the Greek pantheon."
— modified from Understanding appositives and the use of the m-dash ( — )
ps thanks to Dinesh Kumar, for shortening the title. However, I don't see which 40 characters were added to the body. Can you assist?
pps other threads along this line have not resolved this particular point about using both em-dashes and the subordinating single comma. I retain this thread, because it is an example that cannot be fixed by simply moving the subordinate clause, or by dropping punctuation.