Hello, Nathan,
PhotoScan uses EXIF information from the source photos to guess the focal length of the camera. Usually cameras write either FocalLengthIn35mmFilm, or FocalPlaneXResolution and FocalPlaneYResolution EXIF tags.
If your camera writes FocalLengthIn35mmFilm EXIF tag, then you can perform downsampling safely.
If your camera writes FocalPlaneXResolution and FocalPlaneYResolution tags, then the values of these should be also changed in accordance to the scale used when downsampling the photos. Unfortunately, image editing software known to me keeps these tags intact. This leads to improper guess of the camera focal length, which can lead to incorrect reconstruction results.
When both FocalLengthIn35mmFilm and FocalPlaneResolution tags are present, PhotoScan will use information from FocalPlaneResolution tags.
In the latest version of PhotoScan there is an option to specify the camera calibration manually, using the Camera Calibration... dialog from the Tools menu. Using this dialog you can override EXIF information used by the program. Please let me know if more information on this option is required, as it is not covered in the help yet.
With best regards,
Dmitry Semyonov
AgiSoft LLC