Does ProsperOps make changes to my EC2 instances? Could ProsperOps somehow affect my application?

No. ProsperOps only manages Reserved Instances (RIs) and Savings Plans (SPs), which are commitment discount instruments completely independent of the EC2 instances themselves. As such, ProsperOps management tooling has no access or ability to launch, start, stop, or terminate EC2 instances or impact application performance, availability, etc.