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The big question, and I think that I can guess the answer from your question. Are you using pulse guiding via ASCOM (And computer control of your mount) or ST4 guiding via a guder cable from the guide camera to the mount (In addition to the USB cable from the guide camera to your PC)
Assuming you are using pulse guiding and have PHD2 connected to the mount, PHD2 gets the mounts pointing position from ASCOM and if you try to calibrate at more than 20 degrees from the equator it will throw that warning.
If you are using pulse guiding and everything is working OK you do not need to re calibrate for each change of target coordinates. You can calibrate near the equator and zenith and the calibration remains good as you head toward the poles. If your gear does not change (I.E. you do not tear everything down between sessions, changing the relationship between the gude camera and main camera) you can tick the box to auto restore the calibration, calibrate near zenith and equator and then keep re using that calibration until you change something, or you think it may not be working right.
If you do not have PHD2 using a mount connection to determine pointing you need to calibrate at each change of declination (New target) as PHD2 won't know about the change in pointing and the relative rates of RA and Dec movement change when you change declination.
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