You need to gradually eliminate all other possible problems before concluding that.
Do you have a good/charged 7.2V battery on the cortex.
Hook up the joystick to the PC using the orange serial cable, I seem to remember you were using EasyC, go to the download window and do a “vex system info” and verify that you see cortex firmware and joystick firmware versions (probably 3.16 or 3.17 depending on which EasyC you have).
Are the battery voltages good, if the joystick is being powered over the USB A-A cable then it will read around 4.8v, if from the internal batteries then perhaps 7v or above. The cortex should be 7.2v or above.
If all is OK then create a simple program, one analog joystick to one motor and download to the cortex, does the download work? Can you control one motor.
Get back to us with these results and we can determine the next step.
I believed it’s just your joystick batteries being low. This happens a lot for me back when I used to program my VEX robot. Usually if your robot battery or joystick batteries are low, the connection would reset but it is the joystick batteries that would cause the Robot, Game, and Joystick LEDs to light up solid red.
On a rare occasion, it could be the fact your master code is outdated. But if it worked before, then why would not work afterward? If you already reset your joystick, follow the instruction to updating the master code, recalibrating the controller, and establishing a connection with the robot.