I take Vyvanse (lisdexamfetamine) 20 mg everyday. I got a ua done to make sure that I was taking them, but the report came out to be negative. I was only on cirpo for infection. What should I do?

Drug testing . Your physician did a urine test to confirm you have used the medicine. Sometimes it doesn't detect a drug due to confounding meds, supplements, etc. Ask to have a blood test done.
That's great. Well that's excellent. Thanks for that information.
Complete the course. Complete the course of ciprofloxacin as recommended by your physician.