Clean the wood with wood soap and a sponge. If the stain has not penetrated the surface of the wood, this will remove it.
Remove the baseboard with a prybar and hammer. Gently pry the wood away from the wall. Do not over-torque or you will crack the wood.
Sand over the stain with a fine-grit sandpaper. Extend out the edges an inch on either side to blend in your fix later.
Use wood putty and a putty knife to fill in cracks or holes. Match the color of the putty to the color of the wood. Scrape off any excess as you work. Let this set according to the manufacturer's instructions.
Sand the putty with fine-grit sandpaper. The surface of the patched areas should be flush with the rest of the wood.
Apply wood stain with a paint brush over the patched area. Blend it in with the rest of the wood. Let this dry for up to six hours. If more stain is needed, sand the area lightly and re-stain. Sand it one more time.
Apply clear polyurethane with a paint brush over the area. Let this dry for four hours. Sand the surface lightly and apply a second coat.