Based on the community answers, a firmware update is not expected to erase Canon service-center calibration, and Magic Lantern does not wipe those settings.

The reason is that service calibration has often been done mechanically rather than as a simple firmware value. Before in-camera AF microadjustment existed, Canon commonly calibrated bodies and/or lenses by physical adjustment, such as changing mount tolerances/shims, so there may be no user-accessible setting for firmware to overwrite.

In practice, the adjustment could involve the body, the lens, or both, depending on what the service center found during calibration. But from the answers provided, it is unlikely that installing official Canon firmware—or using Magic Lantern—would undo that matching.

If you want complete certainty for your exact model and service procedure, the safest step is to confirm with Canon service, since methods can vary by camera and lens.