Mark,
Does the following not mean that the counter will maintain its count?
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KL03 Sub-Family Reference Manual
32.2 Introduction
The low-power timer (LPTMR) can be configured to operate as a time counter with
optional prescaler, or as a pulse counter with optional glitch filter, across all power
modes, including the low-leakage modes. It can also continue operating through most
system reset events, allowing it to be used as a time of day counter.
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Do you have a reference which says that the CNR will be reset when a wake-up happens from VLLS3 or VLLS0 to run, because of an interrupt which uses the LLWU to wake up the core?
Regards,
Gaurav.