Also Chara is the one who used to be able to reset.

Undyne while being a robot made by Asgore is still The Captain of The Royal Guard.

Papyrus was convinced by Flowey to go back to The Ruins and take care of humans that could fall.

There was no argument between brothers and Papyrus could come back...

There simply is the matter of...
Alphys is..an amalgamate.

It is a new idea I haven't discovered upon much yet but feels much more daunting and interesting than a lizard in a halloween suit.

Now what does this have to do with Papyrus not being able to come back had he wanted?

The Ruins are not only closed but guarded from the outside, exactly because of this.
This danger of an amalgamate is unleashed in this certain universe.
Ruins had to be taken as a quarantine zone.
No one in, no one out.
What if Alphys absorbed many monsters into herself?
It could be a catastrophe.

Sans has a genocide fight but on pacifist he only pretends to be giving his all.

Act it out?
Sans offers you staying in the underground, which would help with scientific research on human souls.
He has no motive to be a father, but he says he'd like to know you better because you gave him hope. Perhaps become friends.

You are the one who told him Papyrus is safe and Alphys did not harm anyone just yet.