Can having the flu make already existing arthritis symptoms worse - i. e., sore knuckles?

Yes: Viral infections can exacerbate preexisting arthritis and short courses of anti inflammatories may be necessary, if tolerated and providing no contraindication.

Fever: Fever associated with any infection lowers the pain tolerance. It should get better with resolution of infection. You may take acetaminophen for the pain, no more than 4.0 grams/day. Keep hydrate with water and juice.