Upvote:3
No, by definition a stopover is a point in your trip where you really stop:
This is different from a layover where luggage is checked through, you are usually expected to stay airside, and as much as possible they'll give you the boarding passes for all flights.
Etihad's online check-in opens 30 hours before departure. Even if they have a bit of additional margin at check-in, between the 39 hours, the duration of the first flight, and how much in advance you check-in for the first flight, it's very very unlikely you'll be able to get boarding passes for the second flight.
The fact that you mix "layover" and "stopover" makes me wonder what your intentions are, i.e. whether you actually want a stopover, in which case I'm not sure why you would need the second boarding pass that early -- you can always check-in online during your stay, or you wanted a layover, in which case I don't know why you have such a long wait between flights.