How big is his free-roam area? If it’s more than one room he prob needs a box in each room. It can also help to restrict the space temporarily (to maybe an x-pen size area most of the time with exercise periods of a larger space) and basically start from scratch with litter training. Then you can gradually increase the space and see how he does.
He also might be re-marking the old areas even though he’s neutered if he can smell them. I had an issue with my girl continually marking this one spot. I was cleaning it with vinegar but she would still remark it. Then I realized the area smelled SO strongly of vinegar that I think that was actually triggering her to mark it. I ended up using a carpet shampooer with a pet-safe enzyme type cleaner and she finally stopped marking that spot!
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The answers provided in this discussion are for general guideline purposes only. The information is not intended to diagnose or treat your pet. Seek the advice of your veterinarian or a qualified behaviorist.