[Tyabann]

Originally Posted by Kogetsu Shirogane

Spoiler for ...:

Except Yuki isn't a humanoid interface, Mikuru isn't a time traveler, and Kyon is doomed to go crazy for three days before doing a convoluted amount of time travel, only to die by Ryoko's hands. You know, except that's not how it happened, because versions of those three that shouldn't exist stopped Ryoko from actually killing Kyon and then "fixed things."

Spoiler for sigh:

But they fixed it, so those three days never actually happened. They only exist in Kyon's memory.

What Yuki did was use Haruhi's powers to change the timeline, something only those powers can do. By restoring the timeline, they made it so those three days never happened.

It's exactly what you said. It never happened, so there shouldn't be any problem, right?