The way I see it, you are taking off enough material to remove the flat edge of the board. If that is the case, the outfeed fence needs to be shimmed out by the same amount as the material you are removing.
To set this up, router about a quarter the length of the board, holding it tight against the infeed fence. Carefully back the board out, still keeping it tight against the infeed fences. Now turn off the router. Now with the router off, place the board back on the table, at the place where you had previously stopped cutting (about a quarter the length). Make sure the board is tight against the infeed fence. You will notice a slight gap between the routed board and the outfeed fence. This is the amount the outfeed fence needs to be shimmed out.
Hope this helps.