I'm really happy for you that you were 'found' this site!! You will find tons of help from people who greatly desire to help & share info!! Not to mention the friendships that are formed here!!!
As far as Lyme being in joints, muscles, and anything else that it chooses to destroy - it can be found in MANY different places.
Personally, I have Lyme arthritis (along with many, many other issues) & my current doc has no clue as to what to do to give me any relief.
I have read that LD as an amazing ability to hide itself from ANY tx that a person may be trying to use.
Unfortunately, I even ended up with a brain infection - fun fun!!!
Also very unfortunate is that what you wrote about your sis - it sounds pretty much like LD - & she could already be considered 'chronic' by now. =( =(
I do believe that most of the answers that you & your sis are needing can be found right here on HW!!
Wishing you & your sis health & peace ~
"Conditions": Lyme Disease, STARI, RMSF, Hashimoto's Thyroiditis, Lyme Arthritis, Neuro LD, FM, Chronic/acute EBV, IBS-C, Diverticulosis (& "itis") & now Lyme arthritis (?).