The presence of fault scarps is a first-order criterion for identifying active faults. Yet the preservation of these features depends on the recurrence interval between surface rupturing events, combined with the rates of erosional and depositional processes that act on the landscape. Within arid continental interiors single earthquake scarps can be preserved for thousands of years, and yet the interval between surface ruptures on faults in these regions may be much longer, such that the lack of evidence for surface faulting in the morphology may not preclude activity on those faults. In this study we investigate the 50 km-long ‘Toraigyr’ thrust fault in the northern Tien Shan. From palaeoseismological trenching we show that two surface rupturing earthquakes occurred in the last $39.9\pm 2.7\; ka$ BP, but only the most recent event (3.15–3.6 ka BP) has a clear morphological expression. We conclude that a landscape reset took place in between the two events, likely as a consequence of the climatic change at the end of the last glacial maximum. These findings illustrate that in the Tien Shan evidence for the most recent active faulting can be easily obliterated by climatic processes due to the long earthquake recurrence intervals. Our results illustrate the problems related to the assessment of active tectonic deformation and seismic hazard assessments in continental interior settings.