Superradiant instability of rotating black holes (BHs) leads to the formation of a cloud of ultralight bosons, such as axions. When the BH with the cloud belongs to a binary system and is in an inspiraling orbit, the resonant transition between the axion's bound states can occur. We study the history of the evolution of the binary system accompanying the cloud composed of the fastest growing mode, and its impact on the observational signatures, especially for small mass ratio cases. In this case, the hyperfine resonance, which has a very small resonance frequency, is relevant. Therefore, due to the long timescale, we should take into account the decaying process of axions in the transition destination mode, the backreaction to the orbital motion and the central BH, and gravitational emission from the cloud. We present a formulation to examine the evolution of the system around the resonance and useful expressions for the analysis. As a result, we found the mass of the cloud that can remain after the resonance is, at most, about 10 −5 of the central BH. The maximum remaining cloud mass is achieved when the mass ratio of the binary is q ∼ 10 −3 . In addition, we show that the resonant transition hardly changes the BH mass and spin distribution, while the associated modification of the gravitational wave frequency evolution when the binary pass through the resonance can be a signature of the presence of the cloud.