6 Month Old Regression???

Don't worry - regression is common.  Go back to the puppy routine (confinement, supervision, frequent wee breaks, super great treat for "going" outside etc) and don't feel mean about it, its the best way to get him back on track.  He'll get there.
 
What are you using to clean the carpet?  It should be a biological cleaner.  If you use one specifically for pet mess it should be ok.
 
Is he neutered?  It may have an impact.  But marking behaviour is seen in neutered and unneutered animals and is often linked to insecurity as well as hormones.  Hes reassuring himself that this is his place.  So have some clearly defined boundaries and rules and routines for him, use NILIF...... and keep the bedroom door shut for the time being!

I agree, regression is expected. Pull back the freedom just a bit, and by the time he's an adult he will be able to have run of the house if you wish. We didn't let our dog stay home uncrated until she was 9 months old.
 
Does the dog spend much time in that room with your family? Sometimes dogs decide certain rooms are not "part of their den" based on the fact that they don't eat, sleep, or play in there. We had this issue with our basement - we don't spend much time down there with the dog so she thought it was "not part of the home" and did her business down there. I started playing more down there with her, and feeding her every meal down there, and the problem went away.

I agree - it's time for this dog to be neutered if not already.  My guess is this is simply "teenager" time starting and he likes your 3 1/2 year old and considers him HIS. 
 
In addition to kinda hauling back to Housetraining 101, I would also begin to do some "Nothing In Life Is Free" and in particular, I'd make sure he KNOWS the 3 1/2 year old is also his 'alpha' -- not his property, but his boss!  Even a 3 1/2 year old can help you hand feed this pup and command the pup to 'sit' and do some very elementary things -- you can't eat til you sit, and sit nicely while the 'alpha' puts down his bowl and THEN he eats when told he can BY the 3 1/2 year old.  All very good exercises that can help put things in their proper place.
 
Don't let the dog 'see' you clean up.  I find this has more truth than we'd like to admit -- it is somehow reinforcing to them to SEE us handle their waste.  And if you've never tried it, pick up the waste in a paper towel and 'move' it outside.  Then go take the dog ON LEASH first to the 'scene of the crime' and simply a "No, not here!" and then walk briskly to that place OUTSIDE where you have moved the waste (paper and all) and 'show' him -- "Yes, HERE -- I put it here! Pee/poop *out* side."

this is probably related to you not having completely destroyed the smell--  you actually have to use an enzymatic cleaner to destroy the molecules.  The reason why he had an accident in there in the first place, who knows. I'd clean it well, and keep the door to that room shut for a few weeks when you aren't around, and try spending some time in that room with the dog every day under supervision.
 
But really, 6 months is way too young to give him free run of the house. He's about to enter the "destructo teenage months". Best to limit a dog's freedom for the entire first year. Lots of people think their 4 to 6-month-old dog is fully housetrained, and give them free run, and then they come home one day to find the house trashed.

Shut the bedroom door.