They heard it, but they didn't want to believe it.
All of Aperture technology with some form of sentience also had auditory inputs, so yes, they all heard their queen say farewell to the human woman, but they didn't want to believe that she would actually be gone. Chell had lasted longer than most test subjects; she had outmaneuvered the crushers and outwitted the Turrets, dodged and ducked and rolled with a fierce determination to her goal, whatever that was. The Turrets didn't even hate Chell for knocking them over. They had been fine once GLaDOS had rebooted them remotely, or sent them away to have their bullet cartridges fixed. They rather liked her; she stayed, unlike the others. She was familiar.
That is, until She told her to leave.
Blue and Orange replaced her in the testing tracks. The Turrets greeted them with a melodic hello, and the panels shifted their weight to allow access. GLaDOS made sure Aperture ran as fit as a fiddle, even after she was gone, but that didn't mean Aperture ran the same. It would never be the same, after what happened. GLaDOS had tried to fix the Frankenturrets as well as she could, but some of the Turrets still shook or hopped around. Wheatley had been miserable and awful while in control, and Aperture had never breathed a bigger sigh of relief when their sarcastic but dedicated A.I. queen returned to her rightful place.
But now even the panels didn't spin like they used to...when she was there.
Aperture Science, despite all best intentions, was sluggish at best. The machinery just didn't see any point to go on, lacked motivation in their circuits. What was the point? Who could challenge them like she could? Who could possibly replace her? Not the new test subjects, who were too brain-damaged to do anything. They weren't like her.
One day, someone knocked on the shed door.
"Sheeee's back!" a defective turret drawled.
"She's back," the working turret beside him gasped.
"She's back!" the Adventure Core yelled.
"Fact: she's back," the Fact Core added.
"She's back!" ATLAS and P-Body chattered excitedly in unison.
"She's back," GLaDOS breathed.
Chell smiled.
It looked like Aperture had missed her, too.
A/N: First Portal fanfic! I hope I got all the sentient Aperture tech, minus Space and Wheatley.
I like to think Chell has become a part of Aperture, so much that when she leaves, it feels like a part of Aperture left with her.