If my opponent has cyber blader on his field and i have 3 monsters on my field i know that it's not affected by monster, magic, or trap effects. Next i flip one of my f/d monsters into attack mode and it's penguin soldier, now if i use his effect and remove penguin soldier and then cyber blader would it still work since i wouldn't have 3 monsters anymore.

You won't beable to activate penguin soldier's effect in the first place, because you have three monsters. Though, I could be wrong.

Cyber blader is not just unaffected by monsters, spells, and traps, he negates the effects of those cards.

Cyber Blader isn't unaffected by anything, period...

Penguin Soldier's effect would end up negated and wouldn't return any monsters at all because of Cyber Blader's effect...

Cyber Blader
Earth/Warrior/7/2100/800
"Etoile Cyber" + "Blade Skater"
A Fusion Summon of this card can only be conducted with the above Fusion Material Monsters. While your opponent controls only 1 monster, this card is not destroyed as a result of battle. While your opponent controls only 2 monsters, double the ATK of this card. While your opponent controls only 3 monsters, this card negates the effects of your opponent's Spell, Trap, and Effect Monster Cards.

...so since returning monsters is not a cost of any kind, but Penguin Soldier's effect, it ends up negated and you would've wasted the FLIP: Effect...

Remember, you wouldn't have 3 monsters until AFTER Penguin Soldier's effect resolved. Because you would still have 3 monsters until that point, Cyber Blader's effect would totally negate Penguin Soldier's effect. You need to make sure you understand what's going on in "time order" ("chronologically") to keep everything straight.

Also, a more general response for this thread - keep in mind that Cyber Blader's effect isn't that she's unaffected - it's that she completely negates the effects. That is a big difference if the Penguin Soldier was trying to return some other monster other than Cyber Blader. If Cyber Blader was just unaffected, then the Penguin would work just fine, but since that's not what Cyber Blader does...she completely negates all the effects, the Soldier would be a sad Penguin :)

That's why if Penguin Soldier were a cost, it'd be different (since costs are paid in order to activate the effect and Cyber Blader only negates effects, not activations).

That's why, for example, you could have 3 monsters on your side of the field and be able to activate Mystik Wok. Since you Tribute a monster for the cost of Mystik Wok's activation, it'd take place before the efect attempts to resolve. However, after the cost is paid, there are only 2 monsters on your side of the field, meaning Cyber Blader's effect immediately changes so it doubles its ATK instead of negating effects so Mystik Wok will allow you to gain LP.