Finally had The Talk with W. It went something like this:

W: “Remember there was an earlier episode where Kes was bouncing back and forth in time, and she was talking about the Year of Hell? That’s THIS episode! But it’s wrong! She needed to scan the frequency of the torpedo, and now she’s not there! They should see Kes!”
Me: “But the reason Kes was bouncing through time was that she was irradiated by the chronoton particles of that torpedo. But she’s already left the ship, so she’s not there to get irradiated, so she’s not bouncing through time anymore.”
W: “But it’s wrong!”
Me: “Don’t try to understand the temporal mechanics of Star Trek — it doesn’t work.”

Kids gotta learn the hard lessons some time, and it’s better than her learning it on the streets.