This is the code. The /// are where I added the countdown. Unfortunately the countdown only goes down 9 seconds. What I want it to do is go down the full 24 hours. I have been trying to fix this error for months with no luck.

int beeper_pin = 2; //Naming buzzer pin
int resetGarden_pin = 3; //Naming the warning led pin
int pump_pin = 6; //Naming the pump pin
#include <LiquidCrystal_I2C.h> // Driver Library for the LCD Module
LiquidCrystal_I2C lcd(0x27, A4, A5);
void clearLCDLine(int line)
{
 lcd.setCursor(0, line);
 for (int n = 0; n < 20; n++) // 20 indicates symbols in line. For 2x16 LCD write - 16
 {
 lcd.print(" ");
 }
}
void beepWarning() { //Makes beeping a subroutine
 lcd.setCursor(0, 0);
 lcd.print("WARNING");
 delay(100);
 lcd.setCursor(0, 1);
 for (int x = 0; x < 3; x++) {
 lcd.setCursor(0, 1);
 lcd.print("WATER PUMP ACTIVE");
 delay(100);
 clearLCDLine(1);
 lcd.setCursor(0, 1);
 lcd.print("WATER PUMP ACTIVE.");
 delay(100);
 clearLCDLine(1);
 lcd.setCursor(0, 1);
 lcd.print("WATER PUMP ACTIVE..");
 delay(100);
 clearLCDLine(1);
 lcd.setCursor(0, 1);
 lcd.print("WATER PUMP ACTIVE...");
 delay(100);
 clearLCDLine(1);
 }
 lcd.setCursor(0, 1);
 lcd.print("WATER PUMP ACTIVE...");
 for (int x = 0; x < 3; x++) { //Repeats 3 times
 digitalWrite(beeper_pin, HIGH); //Turn on buzzer
 delay(100); //Delay of 400 milliseconds
 digitalWrite(beeper_pin, LOW); //Turns off buzzer
 delay(100); //Delay of 400 milliseconds
 }
}
void SOSWarning() { //Makes SOS a subroutine
 clearLCDLine(1);
 lcd.setCursor(0, 0);
 lcd.print("WPA Reset Aerogarden");
 for (int x = 0; x < 3; x++) { //Repeats 3 times
 for (int d = 0; d < 3; d++) { //Repeats 3 times
 digitalWrite(beeper_pin, HIGH); //Turn on buzzer
 delay(200); //Delay of 400 milliseconds
 digitalWrite(beeper_pin, LOW); //Turns off buzzer
 delay(200); //Delay of 400 milliseconds
 }
 for (int a = 0; a < 3; a++) { //Repeats 3 times
 digitalWrite(beeper_pin, HIGH); //Turn on buzzer
 delay(400); //Delay of 400 milliseconds
 digitalWrite(beeper_pin, LOW); //Turns off buzzer
 delay(400); //Delay of 400 milliseconds
 }
 for (int d = 0; d < 3; d++) { //Repeats 3 times
 digitalWrite(beeper_pin, HIGH); //Turn on buzzer
 delay(200); //Delay of 400 milliseconds
 digitalWrite(beeper_pin, LOW); //Turns off buzzer
 delay(200); //Delay of 400 milliseconds
 }
 delay(500); //Delay of 500 milliseconds
 }
}
void weekDelay() { //Makes waiting for a week a subroutine
 clearLCDLine(1);
 lcd.setCursor(0, 0);
 lcd.print("Waiting One Week");
long hour = 23, minute = 59, second = 59;//second //////////////////////////
long countdown_time = (hour * 3600) + (minute * 60) + second; ///////////////////////////////////////////////////////////////////////////
 long countdowntime_seconds = countdown_time - (millis() / 1000); /////////
 
 if (countdowntime_seconds >= 0) { ///////////////////////////////////////////////
 long countdown_hour = countdowntime_seconds / 3600;
 long countdown_minute = ((countdowntime_seconds / 60) % 60);
 long countdown_sec = countdowntime_seconds % 60;
 lcd.setCursor(4, 1);
 if (countdown_hour < 10) {
 lcd.print("0");
 }
 lcd.print(countdown_hour);
 lcd.print(":");
 if (countdown_minute < 10) {
 lcd.print("0");
 }
 lcd.print(countdown_minute);
 lcd.print(":");
 if (countdown_sec < 10) {
 lcd.print("0");
 }
 lcd.print(countdown_sec);
 }
 delay(500);///////////////////////////////////////////////////////////////
 delay(500);
 delay(86400000);
 clearLCDLine(0);
 lcd.setCursor(0, 0);
 lcd.print("Waiting Six Days");
 delay(86400000);
 clearLCDLine(0);
 lcd.setCursor(0, 0);
 lcd.print("Waiting Five Days");
}
void pumpOn() { //Makes turning on the pump a subroutine
 clearLCDLine(1);
 lcd.setCursor(0, 1);
 lcd.print("PUMPING");
 delay(100);
 digitalWrite(pump_pin, HIGH); //Turning on the pump
}
void pumpOff() { //Makes turning off the pump a subroutine
 digitalWrite(pump_pin, LOW); //Turning off the pump
 clearLCDLine(1);
 lcd.setCursor(0, 1);
 lcd.print("WATER PUMP OFF");
 delay(100);
}
void setup() {
 //run once:
 lcd.backlight();
 lcd.init();
 lcd.setCursor(4, 0);//////////////////////////////////////////////////////
 lcd.print("HH:MM:SS"); //////////////////////////////////////////////////
 lcd.clear(); // Clear the screen
 lcd.setCursor(0, 0);
 lcd.print("Aero_Pump V3");
 delay(1000);
 lcd.setCursor(0, 1);
 lcd.print("By Alex");
 delay(1000);
 pinMode (beeper_pin, OUTPUT); //Setting outputs
 pinMode (resetGarden_pin, OUTPUT); //Setting outputs
 pinMode (pump_pin, OUTPUT); //Setting outputs
 lcd.clear(); // Clear the screen
 digitalWrite(resetGarden_pin, LOW); //Turning off the reset garden light
 beepWarning(); //Beeps a warning
 pumpOn(); //Turns on the pump
 delay(3000); //Adds a delay of 24000 milliseconds
 pumpOff(); //Turns off the pump
 weekDelay(); //Waits a week
 beepWarning(); //Beeps a warning
 pumpOn(); //Turns on the pump
 delay(135000); //Adds a delay of 48000 milliseconds
 pumpOff(); //Turns off the pump
 weekDelay(); //Waits a week
}
void loop() {
 SOSWarning(); //Beeps an SOS warning
 pumpOn(); //Turns on the pump
 delay(48000); //Adds a delay of 48000 milliseconds
 pumpOff(); //Turns off the pump
 for (int x = 0; x < 3024000; x++) {
 lcd.backlight(); // turn on backlight.
 delay(100);
 lcd.noBacklight(); // turn off backlight
 delay(100);
 }
 lcd.backlight(); // turn on backlight.
}

This is more specifically what needs to be fixed:

long hour = 23, minute = 59, second = 49;//second //////////////////////////
long countdown_time = (hour * 3600) + (minute * 60) + second; ///////////////////////////////////////////////////////////////////////////
 long countdowntime_seconds = countdown_time - (millis() / 1000); /////////
 
 if (countdowntime_seconds >= 0) {
 long countdown_hour = countdowntime_seconds / 3600;
 long countdown_minute = ((countdowntime_seconds / 60) % 60);
 long countdown_sec = countdowntime_seconds % 60;
 lcd.setCursor(4, 1);
 if (countdown_hour < 10) {
 lcd.print("0");
 }
 lcd.print(countdown_hour);
 lcd.print(":");
 if (countdown_minute < 10) {
 lcd.print("0");
 }
 lcd.print(countdown_minute);
 lcd.print(":");
 if (countdown_sec < 10) {
 lcd.print("0");
 }
 lcd.print(countdown_sec);
 }

This is some edited code that I have tried but might have made a mistake on because it does 0 days instead of 7 and (Hours/Min/Sec) 04:09:36.

void weekDelay() { //Makes waiting for a week a subroutine
 clearLCDLine(1);
 clearLCDLine(0);
 lcd.setCursor(0, 0);
 lcd.print("Waiting One Week");
 unsigned long start = millis();
 unsigned long week_secs = 7 * 24 * 3600;
 unsigned long countdowntime_seconds;
 while (countdowntime_seconds = week_secs - (millis() - start)/1000){
 char buff[80];
 unsigned long countdown_day = countdowntime_seconds / 3600 / 24;
 int countdown_hour = (countdowntime_seconds / 3600) % 24;
 int countdown_minute = ((countdowntime_seconds / 60) % 60);
 int countdown_sec = countdowntime_seconds % 60;
 sprintf(buff,"%1d days, %02d:%02d:%02d",
 (int) countdown_day, 
 countdown_hour, 
 countdown_minute,
 countdown_sec
 );
 Serial.print(buff); 
 clearLCDLine(1);
 lcd.setCursor(2, 1);
 lcd.print(buff); 
 delay(1000);
 }
}