@peemee One thing I learned a while ago is that when you've had pain for a long time, the pain centres in the body can become over-sensitive and start firing when there's no danger of injury. The latest advice seems to be to keep working and conditioning the painful bits rather than rest every time you get pain. The human body is strong and resilient and you're unlikely to do permanent damage with normal exercise. A physio sent me some links about it and some of the testimonials were people saying 'I wish I'd known about this years ago'. Of course, this doesn't apply if it's pain caused by a disease like lupus or arthritis. Exercise won't magically fix that.
Does this sound consistent with what you were told during your recent rehabilitation?