The calibration (at least on Hayward GoldLine) corrects the average samples Salt reading on the main display as when it is initially installed it is an average of recorded instantaneous readings.
If you had the system powered up when you changed the water it would have read ~0 salt for sometime and hence would require many readings at "proper" level before the display would properly reflect the current salt level.
I discovered this after opening my pool this spring. My PB had over salted my pool at installation last year and since he had no clue how to setup the SWG properly, the display read 2500 all season.
After pumping down and topping up twice (other issues) it was still reading 2500 this spring, when the pool store was reporting 1200.
Research lead me to here, and the process to view last instantaneous measurement, and resetting the unit.
That said, the "low salt" alert on a Hayward is a separate alarm LED that reports on the "current" state, rather than the displayed average, and will illuminate regardless of "calibration".