If I wanted the profile, I would not use the fil raster; I would use the rawdem raster. However, if the canyon is getting filled and it shouldn't be, there may be something "blocking the flow" at the end of canyon when you run the fill sinks tool.
Do this. In the Layer Properties for the rawdem, under the Symbology tab, make sure the you are using the streched option. Then, scroll down the statistics settings. Change the drop down option to "For Current Display Extent". With this setting, when you zoom in the stretched color ramp uses the current display extent to set the colors for each grid. This gives you more resolution and you can see the nuances in the dem. Change the color ramp to something with several colors to add variability.
Now, zoom to the end of the canyon and. You should be able to clearly see what is "blocking" the flow and causing the canyon to fill. To remedy this, you can put a line (agreestream) in at that location and use it to "burn" in the stream just at that crossing using the DEM reconditioning step. When you run the fill sinks tool, the canyon should not fill. The burned in stream, which likely burns the dem below the canyon bottom, should fill in to match the lower end of the agreestream line. Then you can go through and create the drain lines and use those to do your profile in conjunction with the rawdem.
