Do you have a regular concave crowning file, one of the full concave ones? It's designed to do what you are asking: round off the two edges of the fret without touching the top center. If you are cutting the top center, it means that you have filed too far, without watching your progress.
Most of us first wipe the top of the fret with a black Sharpie, leaving a wide black ink along the top of the fret. Then start filing with the crowning file. It will start cutting the edges first, and as it cuts, the black line gets straight on the edges, and then gets narrower. As you file, watch the width of the black line. When the line gets down to about a pencil line width, like 0.025-0.030" wide, that's when you stop filing. That's the indicator that you have filed down the two corners, but left a narrow little strip of the top center untouched. The fret is correctly crowned.
If you keep going, and the black line disappears, then you have gone too far and damaged the top center strip. You've messed up the leveling. You have to back up and level the tops of the frets again.
You can do this process without the black Sharpie, but you have to watch real close, with magnifier glasses. Look at the shiny flat line along the top of the fret. Before crowning, it's wide in some areas and narrow in others. As you file with the crowning file, you want to make the line all narrow and even in width, across the fret. But don't make the little flat line disappear. The black ink just helps you to see the flat line from farther back, without magnifiers.
Tool note: I've found that the Milwaukee Tools version of the "Sharpie" works even better for this job. The black ink sticks better to metal than the office-supplies type real Sharpie ink.
The
Stew-Mac Z-type crowning file is something different. It's made to shape the fret into a pyramid with a teeny flat at the top, rather than the traditional rounded dome. Some people like their frets like that, personal taste. But the Z file will also damage the little flat line on top, if you go too far.
When crowning frets, you have to pay close attention to what you are doing. And know when to stop.