Focal length is the same for all visible wavelengths of light; otherwise chromatic aberration is obvious in the image. As long as your lenses provide chromatic correction in the near infrared region as well as the visible region, then your images will still be sharp in all colors, and using Spyder LensCal will work as expected. If you find that a particular lens, or a particular lens at a particular setting, produces unsharp images, even when manually focused, you may have chromatic aberration issues, instead of autofocus issues, so keep an eye out for such results.