I'm in the same boat. Was training well for a century and upcoming sprint tris, then a bladder dilemma (still not sure what happened, maybe nerve pull) and now super flu. I could not even got out of bed yesterday, today meh... went to doctor and was given tamiflu and antibiotics. I am hoping that when I feel normal my base will still kinda exist. Mines in my sinuses so breathing just hurts. I have been doing squats and core exercises in the house, just basically pliometrics. Your base sounds great so I bet you'll bounce back quick, just don't stress your lungs. I wish you well and feel better soon.