Allow the flush panel door to dry completely. If the temperature outside is below 60 degrees Fahrenheit, dry the door panel with a hair dryer or heat gun.
Sand the flush door lightly with a sanding block and medium-grit sandpaper. You want to remove as much destroyed wood without causing a valley in the flush panel. If the flush panel door is pressboard, continue sanding until you get to dry pressboard.
Fill in small cracks or holes with wood putty and a putty knife. This helps protect the interior insulation of the flush panel door section as well as prevents moisture from getting into the unfinished wood framing.
Wipe all sanding dust off the wood panel. Paint or stain the sanded section with the same color paint or stain as the door. Over paint the area with a roller or brush to blend the repair with the surrounding good wood.