Obviously there's no way I can be more articulate than a Smogon article, but I'll try to explain it as best as I understand.
Let's say you're setting up to sweep your opponent, but they have a hard counter to your set, which can not only live a hit from your Pokemon, but KO it right after. In such a case, you'd rather switch out, losing your +1 or +2 boosts, to preserve your Pokemon for later. You will switch in to another (defensive) Pokemon which can take the hit meant for the (sweeper) Pokemon you just switched out. Now, suddenly, you went from offensively pressuring the opponent, into a much more passive stance where you are defending rather than attacking. This is a change in the flow of the battle, and is referred to as losing momentum. Now your opponent can force you to play around their strategies and try to predict what steps you have to take, making the battle tougher for you.
Whereas, if you were to use a move such as Volt Switch, U-turn, Flip Turn, or Teleport, you are dealing damage, breaking sashes and switching out to a Pokemon better suited to handling the opponent. Presumably, the boosts you had set up would inflict more damage on the opponent, and while you're still losing the boosts, you have some chance for counter play because you haven't lost a turn in switching and forced into a defensive play style.