While calibrating the machine, the Z-axis fully extended and cut 3 sides of a 2 foot square through my 3/4" plywood, as well as a line from the center to the first corner of the square (top left). It did not raise or lower the Z-axis, after the initial full extension, and did not effectively give me lines to measure for the calibration process.
It’s very possible that you stripped out the orange router on the router, which
would prevent it from retracting.
It sounds as if either the zero wasn’t set, or the Z axis config was incorrect.
go back to the earlier steps where the Z axis is defined and check the settings