...I don't want to put it in timer ISR as it will defeat the purpose of Watchdog Timer.

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As a general practice, we should avoid putting WDT service call inside an interrupt, nonetheless, servicing WDT in an interrupt is NOT a taboo if you have a reason to do so. Sometimes people refer to this type of activities as "partial service", meaning that the service to WDT inside an interrupt will only be performed under certain conditions. For example, the condition can be - WDT will only be serviced when the background code has serviced it previously.