Before you start sanding your saddle down, it is important to be sure you have the truss rod adjusted optimally for your playing style. Excess relief in the truss rod will make the action higher, particularly from about the 4th fret to the fret closest to the sound hole. You might be able to attain a lower action by adjusting the truss rod to flatten out the neck a little more.
You want to confirm proper adjustment of the truss rod first, because adjustments to the truss rod are reversible (if you get fret buzz you can turn adjustment nut the opposite way until the buzz is gone). If adjusting your truss rod yourself, you must be careful not to overtighten and damage either the truss rod and/or the neck and you must be careful to use the correct truss rod wrench and insert it fully to avoid stripping the inside of the adjustment nut.
The only way to reverse excess sanding of the saddle is by adding a shim - but adding a shim will compromise the tone transfer from the saddle to the sound board and is not a desirable solution.
To flatten the neck out (take out excess relief or bow) you need to tighten the truss rod by turning it clockwise. This will compensate for the string tension that works to make the neck bow.
After you have adjusted the truss rod, if you still want the action lower, you can sand down the saddle by placing sandpaper flat on a piece of glass and moving the underside of the saddle back and fourth across the sandpaper using a sawing motion. The glass will create a perfectly flat surface. It is important to keep the underside of the saddle uniform and even so that the saddle will maintain even contact with the soundboard.
You don't have to remove the strings completely to remove the saddle. You can just loosen them a great deal and leave the strings wrapped around the tuning posts and remove the bridge pins. Leaving the strings in place makes it easier to reinstall the saddle to check your progress after only a little bit of sanding. Periodically re-installing the saddle, re-tuning the guitar and checking your progress, will help avoid over doing it. It is tedious and time consuming, but not nearly as much as starting over with a new saddle after you discover you have sanded the existing saddle too much.
It is a good idea to have a spare saddle that matches the one you are starting with, in case you do in fact go too far with the sanding.
Even a pro can take too much off if they are not careful. Just take it slow and sand a little at a time. Also, after you have finished sanding the saddle, you might need to tweak the truss rod a tad as well.