Black hole (BH) spectroscopy has emerged as a powerful approach to extracting spacetime information from gravitational wave (GW) observed signals. Yet, quasinormal mode (QNM) spectral instability under small scale perturbations has been recently shown to be a common classical general relativistic phenomenon [J. L. Jaramillo , Phys. Rev. X 11, 031003 (2021)]. This requires assessing its impact on the BH QNM spectrum, in particular on BH QNM overtone frequencies. We conclude (i) perturbed BH QNM overtones are indeed potentially observable in the GW waveform, providing information on small-scale environment BH physics, and (ii) their detection poses a challenging data analysis problem of singular interest for LISA astrophysics. We adopt a twofold approach, combining theoretical results from scattering theory with a fine-tuned data analysis on a highly accurate numerical GW ringdown signal. The former introduces a set of effective parameters (partially relying on a BH Weyl law) to characterize QNM instability physics. The latter provides a proof of principle demonstrating that the QNM spectral instability is indeed accessible in the time-domain GW waveform, though certainly requiring large signal-to-noise ratios. Particular attention is devoted to discussing the patterns of isospectrality loss under QNM instability, since the disentanglement between axial and polar GW parities may already occur within the near-future detection range.