A pilot project is one that deploys a working system but with the option of taking it out of service, i.e. there is no guarantee that services will be continued forever, and contracts associated usually specify a clear ending date.
Usually a pilot project unites several protototypes to see if one process or service can be reliably delivered by a given group of people using those, to a given set of users. Often the users are chosen specifically to be difficult to support, if the anticipated issue of deployment is the variety of users, or, easy to support, if the anticipated issue of deployment is the technology. The point of the pilot is to show that whatever the hardest issues are, they can be reliably addressed by a full scale operational deployment of the system.