Also, from my understanding I believe that it was 3 earths that were merged: Earth 1, 38 and Black Lighting Earth... which would actually work since we never saw doppegangers from those earths

I think other earths got combined as well but we know for sure they merged 3 earths together to make that an Earth-Prime and other Earths stayed the same or changed during the crisis to a different number/word.

For a Smallville fan like me, Marc Guggenheim mentioned that yes Smallville is still safe! But of course we don't know if they are in a merged earth, a new number earth or the number earth they started with.

So, I just go with the thinking that a lot of earths were destroyed, merged or renenamed.
In the comics, they did the Crisis storyline to merge the earths becuase it was too many lol ...