Should I replace my roof or just repair the damaged spots?

The insurance is apparently ripping you off. I had a little damage to my roof several years ago, State Farm came out and agreed it needed a new roof and covered the cost completely except for the deductible. That roof was almost 15 yrs old. In your case, if you've already been paid and it won't cover the cost, I'd replace the missing ones and pocket the rest of the money. Unless it's leaking it should be fine.