I'm using nRF52840, PCA10056, and finding that if WDT is enabled (but not expired), after a soft reset (NVIC_SystemReset, or a debugger reset) the RTC no longer runs.
If the watchdog expires, or there is a hard reset, then RTC works again. Probably also works after system OFF/NFC wake, but I didn't try.
It looks the same as this ticket, but had no resolution:
https://devzone.nordicsemi.com/f/nordic-q-a/14321/wdt-halts-rtc-after-nvic_systemreset
The issue is reproducible with the nRF SDK WDT example (SDK 17.0, examples/peripheral/wdt):
Replace the wdt init and for() loop in main with the following (changes highlighted):
and add the handler: