We have investigated the topological properties associated with degeneracies of a non-Hermitian Hamiltonian, called as exceptional points (EPs), in the case that three modes are interacting with each other. Even though the parametric evolution of the modes cannot be uniquely determined when encircling more than two EPs once, we can recover the initial configuration of the modes by encircling two EPs three times or three EPs twice. The group theoretical consideration provides some hint on it. We confirm our expectation by numerically calculating the modes of an open quantum system, two dielectric microdisks.