Welcome to the W.E. forum Robbers,
There are 2 ways I’ve done this.
- You can set your guide rod angle to the lowest angle you can achieve on the unbeveled side. Then with an edge leading stroke, that is down and onto the knife edge, pull the 1000 grit (or the finest grit stone you have), down across the burred edge with very light and gentle pressure. You’re just trying to remove the burr with out applying any bevel. It may be easier to hand-hold the fine stone and pull it across the flat side bevel, edge leading, at as acute an angle as you can, while the knife is still clamped.
- You can dismount the knife then apply blue tape to the non-beveled side just right up to below the knife edge. Then with your 1000 grit stone hand-held, pull the stone with gentle/light pressure across the unbeveled edge as flat against the edge as you can, onto the hand-held knife. If you prefer, lay the stone flat on your table top, then pull the knife across the stone.
The light edge leading strokes should remove the burr. This may result in a small micro bevel if the angle was too great or the applied pressure to heavy. You can use a strop across the unbeveled edge afterwards if you like. Be sure to clean the knife well before using a strop.