Urban areas have been dramatically impacted by the sudden and fast spread of the COVID-19 pandemic. As one of the most noticeable consequences of the pandemic, people have quickly reconsidered their travel options to minimize infection risk. Many studies on the Bike Sharing System (BSS) of several towns have shown that, in this context, cycling appears as a resilient, safe, and very reliable mobility option. Differences and similarities exist about how people reacted depending on the place being considered, and it is paramount to identify and understand such reactions in the aftermath of an event in order to successfully foster permanent changes. In this paper, we carry out two analyses, both from a geographical and temporal point of view: on the one hand, we compare the short-term effects of the pandemic on BSS usage in two French towns (Toulouse and Lyon), and on the other, hand we analyze its mid-term effects in Toulouse. We used Origin/Destination data for four years: 2019 (pre-pandemic), 2020 (pandemic before massive vaccination campaigns), 2021 (pandemic after massive vaccination campaigns), and 2022 (year after the pandemic peak). We consider two complementary quantitative approaches. Our results confirm that cycling increased during the pandemic, more significantly in Lyon than in Toulouse, with rush times remaining exactly the same for the four years, even during the lockdowns. The year 2021 shows a transitional profile between 2020 and 2022 that could be attributed to adaptation to living with COVID and perhaps also to the increased sense of safety brought by the vaccination campaign. We also found that trip duration during the pandemic situation was longer both on working days and weekends. Comparing BSS traffic with road traffic and public-transport validations shows that cycling is a resilient mode of transport in a pandemic. Among several general observations, we note that peripheral/city center BSS flow is more noticeable in Toulouse than in Lyon and that student BSS usage is more specific in Lyon.