The patient and very helpful Chuck Westfall, Technical Information Director for Canon US (at the time of writing), has provided a description of the calibration process, which specifically deals with a query from people owning more than one camera body. The information was posted on 1 Aug '03 in a thread on the Rob Galbraith Canon D30/D60 and 10D Forum. (The forum no longer operates; here is the main site.)

Given the transient nature of forum information, here's a summary:

What is the potential impact of calibration when you have multiple bodies and lenses? More specifically, could "correcting" one set of tolerances, possibly upset another?

There is no impact provided all cameras and lenses are properly calibrated. Each component has its own set of tolerances: the calibration procedures for each component are done according to the known specifications for that component, not for one component to match another. Let that one sink in for a minute.

The camera body is first calibrated with a "tool lens". Once the body is operating according to design specifications, the camera can be checked against other lenses. In the case that an auto-focusing error is detected, there are two possible courses of action: adjusting the camera's internal lens information database, or adjusting the circuitry of the lens itself, if it is not operating according to design specifications.

The only way to accurately determine which component needs adjustment is to carry out diagnostic tests. These tests can only be performed by Canon Factory Service technicians, or qualified independent service outlets who have been trained and authorised by Canon. If it turns out that the lens circuitry needs calibration, then the only way it could possibly have an adverse effect on the focusing accuracy of another EOS body would be, if that second  body was itself not correctly calibrated, in which case we go back to square one and calibrate that body with a "tool lens".

To summarise: the reason that calibrating a lens does not damage its performance with multiple camera bodies is because the calibration standards for the lens are independent from the calibration standards for the body. It is certainly possible for an autofocus lens to require calibration, because the lens contains its own microcomputer and many other internal devices such as focusing motors, diaphragm actuators, etc. that report the results of their operation to the lens computer and eventually back to the camera through the electronic lens mount contacts.

Some customers may like to know which component is more likely to require an adjustment, if one is necessary, but that sort of information is confidential and essentially irrelevant to the end result.

3 August 2009 originally published September 2003