The amended line is right at the very end of Remake, after the party battles Sephiroth. We see the paths of Zack and Aerith cross, seemingly from different worlds or timelines, as rain begins to fall.

Aerith looks upwards and states: “I miss it… the steel sky.”

The steel sky in question is the plate the city of Midgar is built on, which the slums lie beneath. It’s poetic, then, and calls back to an earlier line from Aerith that also references the steel sky. Moreover, it parallels both the party and the player’s journey - the adventure will continue in Rebirth, out in the open world and no longer beneath the “steel sky” of Midgar.

Except now that line has been changed to: “This sky…I don’t like it.”

Ostensibly, the new line has the same purpose and has a similar meaning. Aerith still looks upwards and comments on the sky, after all.