"When an opposing character targets a character using this team ability with an attack and misses, modify the defense value of all characters using this team ability by +1 until the end of the turn."

Does the modifier go into effect for a roll that is rerolled via PC?

I.E. - Character X misses Magus (using the UCT ATA) with a close combat attack - the player decides to reroll using PC - Does Magus then modify his defense value by +1 because he was missed by the first roll of the attack?

No. When you make a reroll with Probability Control the previous roll is ignored. So it's as if it was never made.

Probability Control

Mirandir is correct. To be even more thorough, an attack wouldn't be considered a hit or miss until the attack roll is finalized, ie; after all re-rolling is done.