Have you dismantled the printer?,
Have you put the Z stepper cable in the controller board correctly?
I'm assuming there's a separate socket for each Z stepper so two cables..
Your last answer eliminates cables and firmware,
The only way the steppers could move in the wrong direction at the same time is:
Either a wiring fault to both steppers - I have a CR10S-Pro and both stepper cables failed at the connector which meant a bit of delicate soldering.
OR
Firmware which is moving the steppers in the wrong direction - and you say no change
OR
Possibly a Stepper motor driver problem - wouldn't be unknown, having blown drivers myself [caused by overheating].
Going in the reverse direction means the polarity at the stepper coils is opposite to what it should be, if nothing else has changed is the orientation of the cables correct? Odd that it should only affect the Z steppers, I'm not familiar with the cabling to the external control box. But there's nothing else that could send them up when you want down.