Just because something is listed as a potential side-effect doesn't mean the med actually causes it. The lists are compiled from drug trials reports and list everything that is reported, even things that can't possibly be caused by the med such as bacterial and viral diseases. I have been only able to find one case report involving antinuclear antibodies (ANA) and amitriptyline and the AD was used to
treat the condition, not its cause. Like many TCAs, amitriptyline is a potent antihistamine which can significantly ease immune disorder symptoms and may prevent them in some circumstances.
BTW-anxiety and depression are arguably themselves the results of an autoimmune response which kills brain cells in the hippocampal regions of the brain. ADs work by stimulating the growth of new cells - see:
Depression and the Birth and Death of Brain Cells (
PDF) and
How antidepressant drugs act..
A little knowledge is a dangerous thing. You are taking meds which have a far higher risk of doing you harm because of a potential risk which probably doesn't exist.
People have taken both for decades without issue.