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Could a shoulder injury that is related to vaccine from a flu shot (where the vaccine got into a tendon or the capsule instead of the muscle and remains there for a long time) cause disruption to the immune system or an autoimmune reaction (since it is not well vascularized)? Long before COVID I've seen people who've had that. You also sometimes see where it gets into the subcutaneous and dissolves the subcutaneous fat; certain vaccinations are not supposed to go in certain places. I've seen local reactions. In connective tissue, because there's poor vascularization, it heals slowly. It's possible that it could cause an ongoing irritation to the immune system. Trying to judge how much of an immune response you're having to that versus some other things it's pretty tough. It's an immunologic insult to a tissue where the agent was not supposed to go and so in the short term I've seen that it can be immune aggravating at the very least. Trying to figure out how much of a problem it can be is pretty difficult.
Regarding the post vaccine shoulder injury. I would say treatment would be difficult. Especially if it got into connective tissue like the capsular tendon ligament. I would suggest speaking to your own healthcare provider. If people can stand the taste, because topical DMSO is used a lot for joint pain, it does make you have a taste in your mouth because it absorbs so well. It's sulfury. Some people taste garlic or other sulfury things. As long as that's not a problem I've had people use that over the area because it does absorb. We do use it for joint problems. DMSO can be very useful that way. The other thing can be a therapeutic ultrasound from a physical therapist. They can use a pulse setting of therapeutic ultrasound. They use that often to break up adhesions. Sometimes that's useful. Those would be the two things I would think of first. There's some other more invasive things but those would be the two things I think of first.