Are you running the current version of the Firmware? I had this issue with previous versions of the firmware.
FYI - I’ve had a few errors in the past with X, Y, or Z being off after I run a Z Probe operation. It’s been with older versions of the firmware and usually when I had X, Y near the bottom left corner. That lead to me ruining 2 projects (purple heart wood is not cheap). So - my new process is to always verify X, Y home after I probe at bit change.