This question has come up a few times from those using their Kestrel 4000 (and up) series.  

We asked Ben, head of tech support at Nielson Kellerman to help explain it.  He writes:

It's easier to explain by noting how the Kestrel used to work:  as noted in the instructions, the user must start with one known and set that into the Kestrel (if you know your altitude then plug that in as the reference on the Baro screen, and vice versa).  Once that reference has been programmed, the user must take the resulting number (in the case above you would take the Baro number that the Kestrel gives) and go to the other screen and plug that in as a reference.  Now the Kestrel will give you the correct barometric pressure and altitude.

What NK realized is this extra step could be eliminated by including a Sync feature that would do that for the user.  However, the reason it is optional (on/off) is because long range shooters don’t actually want to set their reference altitude to what it actually is, they want to put in a reference altitude of zero.  That gets into the whole issue of what is the reference altitude.

Barometric pressure is the pressure corrected to sea level (over in the UK they call it MSLP – mean sea level pressure, and they call Barometric Pressure what we call Station Pressure).  This is done (I presume) to make sure people in the same area can speak to each other in a sensible way about the local pressure front (imagine getting the pressure from a weatherman at the top of a 50-story building – clearly the station pressure (actual pressure) will be different between the top and the bottom of the building).  Long range shooters want to know the actual pressure where they are because that’s what will affect the local air density and therefore how the bullet behaves.  This market will want to put 0 as their reference altitude so the unit doesn’t perform any barometric pressure corrections.  This is the rational for the ability to turn the Sync on or off.

Hope that helps!!