It is always to sand down either the top or feet of a bridge, as long as the shortening doesn't make the bridge top too thin to support the pressure of the strings. Mark with pencil and then take a sheet of fine carborundum or wet & dry paper (ordinary "sand" paper disintegrates too easliy). Put the paper down on a flat surface, rough side up, and run the bridge (lengthwise) along the paper.
If you are taking some off the top, mark the position of the string slots with pencil marks down the bridge. Once sanded, use a fine triangular needle file - from modellers shops, to re-cut the grooves.
If the new bridge is already useless, you have nothing to lose. If it doesn't work to your satisfaction, then try a different style of bridge.
Alternatively find out if your neck adjustment will increase the angle between body and pot, and so drop the string heigh above the upper frets.
Quack!
Geoff the Duck.