My wife studies and applies pain science in her career, she has several thousand very happy clients. I say this not to brag (although I am proud of her), but to establish some credibility...
So here's a bit of pain science, heavily summarized:
1 - There is a LOW correlation between chronic pain and tissue damage !!!! (Ya really gotta let that idea bounce around in your brain for a while. That seems to go against everything we've ever heard, I know.)
1b - It ain't where you think it is. Our movement system is complex. If you have a sore elbow, it could be because there is some restriction in your shoulder. You never know!!
2 - Our bodies do not really have "pain" sensors. Our tissue can sense things like heat, cold, pushing, and pulling, but not pain.
3 - Our bodies send data to the brain, the brain evaluates the whole context, and decides whether to declare a certain situation "painful".
4 - None of this is to say your pain is not real. Your pain is real !! But often you can minimize or eliminate it.
5 - The brain's top priority is to protect the body. If the brain becomes alarmed or uncertain as to the status of a part of the body, its first defense is to issue pain signals to that body part to make it stop moving. Often this is a great strategy, e.g., it helps damaged tissue heal.
6 - Everyone has a brain-body, proprioceptive "map". This map is based on ongoing communications between the brain and the body. The body is constantly sending data to the brain about what's going on.
7 - To be accurate, the map depends on high quality, ongoing data, much of which comes through movement.
8 - When we get injured, we rightly protect the injured tissue by reducing or stopping movement. This allows the tissue to heal, hooray, but it also causes the map to this tissue to get reduced, and have poor quality data. So back to point 5, if the brain is getting uncertain data, its first strategy is to issue pain signals.
== A scenario
Let's say we sprain an ankle. Real tissue damage. Pain. Immobility. All is as it should be for healing.
But weeks, months, years go by, and the ankle still feels weak and painful. By now the tissue has healed, but the map has been corrupted. Given a bad map, the brain will continue to issue pain signals. So what we have to do is restore the map!!
== A solution for chronic pain
We want the pain associated with that old injury to go away. So in order to restore the map to that tissue, we need to give the brain a TON of data about that tissue. The technique is to do a lot of MOVEMENT EXPLORATION in that area. So if that ankle still hurts, you have to explore all the movements you CAN do with that ankle. An important caveat is DO NOT MOVE THROUGH THE PAIN !! Instead move up to the edge of the pain, and then move around the pain. Try moving from a slightly different direction. Try the same movement with your knee bent, or or hip at a different angle. To reiterate point 1b - we never know the actual source of the pain. If your repaired ankle is sore, it could be that your knee is tight from helping the ankle heal.
So you have to do a lot of movement exploration. Up to and around the pain, not through it!! The more pain free data the brain receives, the more it trusts that the tissue is okay. The more the map is restored.
== Flexibility vs. Mobility
Flexibility is a measure of pain free range of motion, it's not bad. But mobility is better. Mobility is a measure of pain free range of motion UNDER YOUR OWN STEAM. So if your PT can move you in a certain pain free way, but you cannot make that movement on your own, you have flexibility, but not mobility. WE WANT TO MAXIMIZE MOBILITY.
So stretching is an old idea, and an okay one, but stretching is mostly about flexibility.
A new improvement to stretching is called CARs (controlled articular rotations). CARs is basically movement exploration and stretching - but using only your own muscles. So something like downward facing dog relies on a gravity assist, it doesn't count as a CAR. You can find a number of good Youtubes on how to do CARs.