Don't you have a Newton's cradle to experiment with? First off, don't most have 5 balls instead of 4? (at least mine does)
I take it you mean you're pulling up two balls then releasing them, yes, momentum is conserved (it always is). There's two possibilities (plus an infinite number in between): Will two balls on the opposite side move the same distance as the released balls or will only one ball move, but go higher (or some combination in between).
The experimental answer is that two balls on the opposite side move the same distance as the released balls. If you drop 3 balls, three balls move on the opposite side (including one of the dropped balls). If you think about both kinetic energy and momentum, you can see why.
If you mean you're taking one ball out of the sequence, then momentum is still conserved, but ... Have you noticed how the spacing is set so the path of a ball drives right through the center of the next ball? With one ball removed, you strike the ball across the gap at an angle - not a large angle, but definitely not straight through the center.
Experimentally, the balls quickly get out of sync with each other, but, they eventually resync with all the balls going back and forth in the same direction (no neat collisions).
If you do the traditional thing of just dropping one of the end balls, eventually the system loses energy faster than it loses momentum (air resistance, friction, etc provide a small external force meaning energy and momentum can't truly be conserved with the normal desktop model), resulting in all the balls moving back and forth together, but not nearly as far (no neat collisions).
You really should either get one of these things, or at least browse through a gift or science store. That way, not only can you see the conservation of momentum, but you can see where you're losing energy (mine is kind of old and I've had the unhealthy habit of placing business cards or my bottle of "Future Glue" in the cradle - the strings vibrate, which means my balls probably arent' perfectly aligned any more). [But, the Future Glue is pretty cool. You know how if you drop your coffee cup, you can never find all the tiny little fragments to glue your cup back together very well. If you use the Future Glue on your cup the night before you drop it, you don't lose all those little fragments

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Browse the store with you notebook and pencil, of course.
Salesperson: "Can I help you with something?"
Reply: "No, I'm just doing my homework ... Uh, wait, do you remember the formula for kinetic energy?"
Salesperson:
