I believe the computers engaged the change of flight path AFTER the ‘alright, good night’ comment. Perhaps all comm was disabled at that point, as directed by the modified software.
And also note that just because ACARS was turned off, doesn’t mean the knob was turned to the ‘off’ position in the cockpit. It’s like your computer monitor button is ‘on’ but the monitor is really off because the computer is off. This is similar to how ACARS was turned off by the software, even though the knob was probably ‘on’.