Hello.
After each pcb RST (POR or not), the RTC is resetted, because VBTCR1.BPWSWSTP bit is set to 1 after each pcb reset (renesas datasheet section 11.2.1).

I suspect Arduino settings to automatically set this bit at each pcb power restart. How to deactivate it so we can use the RTC function normally ?

We need this VBTCR1.BPWSWSTP bit to be setting at 0 when PCB powering on, otherwise, RTC function is unusable.