In a 3 year old house, I started to finish the basement and noticed moisture on the subfloor above directly under kitchen door. I noticed some discoloration of the grout against the door and when I pry up the plastic trim on the door sill the wood underneath is rotten. Look further and the bottom of the casing is showing deterioration. I see where builder let concrete backer board extend under door sill almost to the edge of the aluminum. This door opens onto a deck, I think that when it rains water splashes from deck to backer board and runs on top of and under it. Am I right on this? How do I fix it? Can I buy a replacement sill and casing or am I going to have to build it? Where could I find a detail to show me how?
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You should take out the door unit to repair (replace) the subfloor. Then install a sill pan on top of the subfloor and the proper head flashing for this door. Install this door or a new unit (if this one has bottom of jamb problems etc). Seal the siding to door casing properly and likewise all areas that water may penetrate.
A half #### 'd approach might be to cut out the alum. threshold and try to repair the subfloor. Fabricate a sill pan using vicor or similar and then install a new adjustible sill. Take a close look at the upper area of the door unit. Water could be coming in at several places. Head casing if not flashed properly, siding/casing and even at the jamb threashold interface.
Without protection and the proper flashing doors can collect water and you'll never see it until you're finishing the basement and happen to remove the insulation often stuffed up in a joist space under the door.
Best of luck.
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It may be possible to remove the rotten sill and replace it without removing the entire door. I did that once on our house, and fashioned a new sill from redwood (though ipe would probably be a better choice). A plastic cover over the wood is an invitation to rot.
Re the deck, generally you need to have a gap between the deck boards and the sill so that water can drain. Think like a drop of water. And, more specifically, think like a drop of water that isn't scared off by a little caulk. The only thing you can't get through is metal, you little drip, you.