Watchdog timer/deep sleep loop for Atmega 328 Pro Mini 5v 16 mhz
I don't know if this is the best solution, but I found a workaround. In the ISR(WDT_vect) function I added a while statement where I added a boolean variable set to true when running the basic program, and false when I enter looping deep sleep mode. I'd appreciate if someone out there can provide a better solution, but for now this one works for me. Below is the revised code in case anyone's interested.
// thanks to KeyChainino for basic code. I added ADC disable to further reduce power from 0.67mA to 0.54mA
//revised by John Bedford 01/12/2020
#include &lt;avr/interrupt.h&gt;
#include &lt;avr/sleep.h&gt;
#include &lt;avr/power.h&gt;
#include &lt;avr/wdt.h&gt;
const int ledPin = 13;
const int resetPin = 9;
volatile boolean wdtInterrupt;    //watchdog timer interrupt flag

// the setup function runs once when you press reset or power the board
void setup() {
  pinMode(ledPin, OUTPUT);
  pinMode(resetPin, OUTPUT);
  digitalWrite(resetPin,HIGH);
  Serial.begin(9600);
  Serial.println(&quot;Resetting..&quot;);
  delay(100);
  watchdogSetup();
}

// the loop function runs over and over again forever
void loop() {
  wdtInterrupt= true;
  digitalWrite(13, HIGH);   // turn the LED on (HIGH is the voltage level)
  delay(1000);              // wait for a second
  digitalWrite(13, LOW);    // turn the LED off by making the voltage LOW
  for(int i=0; i&lt;9; i++){; //set up loop to force timeout of WDT
    delay(1500);
    Serial.print(&quot;Loop &quot;);
    Serial.println(i);
    delay(100);
  }
  wdt_reset();
  
 
  waitSleep(2); //go sleep for x loops of WDT settings (8 sec max per loop)
}

void waitSleep(int sleep_cycles) {
  wdtInterrupt=false;
  while (sleep_cycles) {
    goSleep();
    sleep_cycles--;
  }
}

void goSleep() {
  watchdogSetup(); //enable watchDog
  // disable ADC (analog to digital conversion)
  byte old_ADCSRA = ADCSRA;
  ADCSRA = 0;
  set_sleep_mode(SLEEP_MODE_PWR_DOWN);
  sleep_mode();
  //disable watchdog after sleep
  wdt_disable();
  ADCSRA = old_ADCSRA;
}

void watchdogSetup() {

  //WDP3 - WDP2 - WPD1 - WDP0 - time
  // 0      0      0      0      16 ms
  // 0      0      0      1      32 ms
  // 0      0      1      0      64 ms
  // 0      0      1      1      0.125 s
  // 0      1      0      0      0.25 s
  // 0      1      0      1      0.5 s
  // 0      1      1      0      1.0 s
  // 0      1      1      1      2.0 s
  // 1      0      0      0      4.0 s
  // 1      0      0      1      8.0 s


  // Reset the watchdog reset flag
  bitClear(MCUSR, WDRF);
 
 
 //The following bit have to be set at the same time otherwise the system doesn't set the right value

 /* Start timed equence */
 //Watchdog Change Enable to clear WD (by setting the WDCE bit) and Enable WD (by setting the WDE bit)
 WDTCSR |= (1 &lt;&lt; WDCE) | (1 &lt;&lt; WDE);
 
 //Set new watchdog timeout value to 8 seconds (WDP3 and WDP0 to 1) and enable interrupts instead of reset (WDIE to 1)
 WDTCSR = (1 &lt;&lt; WDIE) | (1 &lt;&lt; WDP3) | (1 &lt;&lt; WDP0) ;
}
void hardwareReset(){;
  digitalWrite(resetPin,LOW);
}

ISR(WDT_vect) {
  while (wdtInterrupt){
   hardwareReset();
  }
}