Gosh, that does seem like a long time. DS has had swelling for many weeks at a time but not that long from what I recall. It flares every few months and is super crepey for long periods - misshapen etc . When in pain, he takes a break from sports and wears various knee braces. At one point they recommended he take round the clock Motrin for a week to see if that reduced swelling. Once the pain goes away, he still wear knee braces because it does stay swollen for a long time. As far as damage - none so far when he's had xrays here and there. He has always resumed sports successfully as long as his knee isn't hurting and so far so good.
I think I would consider trying the Motrin if you haven't already. We also spray magnesium spray on his knee when it's flaring. Not sure how much it helps but it's something.
Parent of 14yo DS with +Lyme test in Nov 2015, co-infections: mycoplasma (strongly +), babesia, mainly with antibiotics/anti-malerials. Supplementing with Vit D, Vit C, Vit B-12, multvitamin, milk thistle, dandelion, nettles, Burbur/Pinella, L acetyl carnitine. Magnesium oil, charcoal led to shorter herxes.
Website I started: ParentsofLymeKids.com