Hi pbourke,
the focal length of a lens can change when adjusting the focus. This is a well-known effect named "focus breathing".
In general, I usually use only manual focus, i.e. I stay at a constant distance to the object-of-interest. If I need some additional close-up shots, where I am required to refocus, I create a second calibration group for the images with the adjusted focus in Agisoft to compensate for the change in focal length.
Hope that helps.
All the best,
Arie.