My daughter has also being diagnosed with amplified pain. The way it was explained to us is that when a kiddo is inflamed for a very long time, the nerves get used to sending pain signals to the brain. So even once the inflammation is gone, they keep sending those pain signals and your child feels pain, even though there is no inflammation any more.
There are several things you can do to help. I would suggest seeing pain management ASAP.
For kids who are not functioning due to amplified pain (miserable, unable to play, enjoy activities, sleep, attend school), there are inpatient pain programs. These combine intensive PT, OT, aqua therapy, psychology (usually cognitive behavioral therapy) etc. to re-train the nerves and to teach the child to live and cope well with chronic pain.
They are not magic cures, unfortunately. Kids get better, but the pain does not go away. But it was a huge help for my daughter. She did a program at Cleveland Clinic. The programs are tailored to each kids' needs. She did two weeks inpatient and one week outpatient.
She was missing school, unable to hang out with her friends and unable to sleep. She'd lie awake till 4 or 5 am in pain. She was always exhausted, always in pain and spent most of her time in her room, because she couldn't do anything.
She was also on a lot of pain medication.
By the end of the program, she was a functioning, happy teenager. She started sleeping normally, eating better and was able to do a full day's worth of activities. It was very intense - 4 hours of PT/OT a day - but it was so worth it. Everyone was wonderful (doctors, nurses, physical therapists, occupational therapists) and it really helped her learn how to cope with chronic pain. Over time, we have reduced her pain medication.
There is a great book that explains amplified pain well "Conquering Your Child's Chronic Pain." You can get it on Amazon. It explains how chronic pain really needs to be treated differently from acute pain - for example, instead of having your child rest every time he's in pain, he should actually stay busy. He should go to school - it will keep his brain distracted and lessen the pain.
The goal is to keep his life as normal as possible. To push through the pain. It sounds horrible and hard and even cruel, but I can honestly tell you it works. My daughter was like your son - she missed so much school in high school. It didn't help anything - it just made her more isolated and stressed out.
The one caveat is that you should make sure that his IBD is under control before you pursue this approach. Has he had a pillcam recently? Or an MRE? Those are more accurate tests than a SBFT.
I would definitely have him continue to see a psychologist - preferably one that has experience with children with chronic pain. Usually when you see pain management, they will have a psychologist on staff that works with these kids. Anxiety and depression do worsen pain so it's very important to see a psychologist.
If he does have amplified pain, I wouldn't expect pain free days. I know this all sounds crazy and as moms, we just want to take the pain away. But this is the best approach for chronic pain and it really does work. Just keep things normal and try to get to pain management as soon as possible.
I would look for a pediatric pain management program specifically - most children's hospitals have them now.
Good luck!