Well, as patients ourselves we are told to finish all of our medication, maybe because it keeps on working even if we feel better. I looked at the website you posted and found this:
Good luck with this, Amelia, FIP is horrible.FAQ
How long is the treatment?
The recommended length of treatment is 12 weeks. However, the actual treatment length may depend on many factors including how quickly your cat responds to the treatment, the gravity of the FIP infection, your cat's breed, age, overall health. Consult your veterarian on the length of treatment for your cat.