I recently started a new character for Dawnguard, and as such have not completed much of the main questline (at Diplomatic Immunity).

In Seeking Disclosure, I had to collect Elder Scrolls for the Moth Priest to read. Discerning the Transmundane, a quest I have not reached yet, is now active, as I had to retrieve the second Elder Scroll.

What should I do? What happens when I reach the latter quest later? I'm very confused, and worried that this could cause issues.

Do the quest. Why do people assume that getting an Elder scroll affects anything? You can get the Scroll from the Dwarven ruins BEFORE ever even starting the MQ so why would this be different?

This.

And you can't ruin the MQ because after you finish either the Dawnguard or the Vampire Quest line, you can't remove the Dragon Elder Scroll out of your inventory until you go through the associated mission on the MQ.

You are not going to mess anything up. You don't even have to start the vanilla Skyrim MQ to get the Elder Scroll (Dragon)...

Okay Uriel. I am going to ask a stupid question. Tell this old lady what vanilla Skyrim is. It is the regular Skyrim game?

Vanilla means basic and unaltered. So no DLC or expansions or mods. Like Vanilla Ice cream with no toppings

Thanks Drake. I guess that I have been playing vanilla skyrim all along. hahaha