I do not have test code, I just tested it using a debugger. All I did - I selected SIRC clock (I do not have a board with XOSC here right now) and I enabled the RTC by CNTEN. Then I can see that the counter is running in RTCCNT:

Then I generated SW functional reset - also by debugger. I set FUNC_RST in MODE_CONF register, then I set MODE_UPD bit in MODE_UPD register and finally I wrote keys to CTL_KEY register. The MCU was reset, I reconnected debugger (hot attach without reset) and I saw that the RTC is still configured and running.
Regards,
Lukas