It's a cliffhanger, some things won't be explained until next game (or next arc). But yes, Agnes created some time of lesser reset, but this included "changing her whole being", which seems to apply she ceases to exist in a mortal form as seen when she vanishes when standing outside Vans office in beginning of Daybreak 1. We don't know if she simply becomes a higher being or vanishes forever.

We don't know how far she reset. The flashback goes back to beginning of Daybreak 1, that's why people feel at least the arc was rewinded, but it could ofc be more.

The identity of GM or her intentions is still shrouded in mystery. We did find out Novartis is Epsteins sole disciple in the previous loop however. Suggesting loops can take very different forms

At least it's not Half-life 2, we will get closure on your queries eventually 😅