The quantum coherence and gate fidelity of electron spin qubits in semiconductors are often limited by nuclear spin fluctuations. Enrichment of spin-zero isotopes in silicon markedly improves the dephasing time T2, which, unexpectedly, can extend two orders of magnitude beyond theoretical expectations. Using a single-atom 31P qubit in enriched 28Si, we show that the abnormally long T2 is due to the freezing of the dynamics of the residual 29Si nuclei, caused by the electron-nuclear hyperfine interaction. Inserting a waiting period when the electron is controllably removed unfreezes the nuclear dynamics and restores the ergodic T2 value. Our conclusions are supported by a nearly parameter-free modeling of the 29Si nuclear spin dynamics, which reveals the degree of backaction provided by the electron spin. This study clarifies the limits of ergodic assumptions in nuclear bath dynamics and provides previously unidentified strategies for maximizing coherence and gate fidelity of spin qubits in semiconductors.