Arduino bug when "myFile = SD.open" is inside loop()
The solution to your problem is to extend your 2 states machine in a multiple states machine.

Declare the enum eState before setup():

typedef enum e_State {
    STATE_START = 0,    // starting the loop (add some initialisation)
    STATE_READ_FINGER,  // Step1: read the finger print
    STATE_DISP_FINGER,  // Step2: display the finger print
    STATE_OPEN_LOGGER,  // Step3: open the log file
    STATE_WRITE_LINE,   // Step4: append a timestamp finger print
    STATE_CLOSE_LOGGER  // Step5: close the log file
} eState;


And update the loop() function with the state-machine:

void loop()
{
    static eState LoopState = STATE_START; // to store the current state

    eState NextState;  // for the next loop

    switch (LoopState) {
    case STATE_START:
        // add additional settings
        NextState = STATE_READ_FINGER;
        break;
    case STATE_READ_FINGER:
        etat = 0; // keep use your 'etat'
        // or return a boolean from your 'getFingerprintIDez()'
        lcd.clear();
        lcd.setCursor(0,0);
        lcd.print("Put Finger");
        getFingerprintIDez();
        if (etat == 1) {
            NextState = STATE_DISP_FINGER;
        }
        break;
    case STATE_DISP_FINGER:
        lcd.clear();
        lcd.setCursor(0,0);
        lcd.print("ID #");
        lcd.setCursor(4,0);
        lcd.print(finger.fingerID);
        NextState = STATE_OPEN_LOGGER;
        break;
    case STATE_OPEN_LOGGER:
        myFile = SD.open("data.csv", FILE_WRITE);
        if (myFile) {
            // record only if file is opened
            NextState = STATE_WRITE_LINE;
        }
        else {
            lcd.setCursor(0,0);
            lcd.print("Can't open file");
        }
        break;
    case STATE_WRITE_LINE:
        myFile.print(rtc.getDateStr(1));
        myFile.print("\t");
        myFile.print(rtc.getTimeStr(1));
        myFile.print("\t");
        myFile.println(finger.fingerID);
        myFile.flush();
        NextState = STATE_CLOSE_LOGGER;
        break;
    case STATE_CLOSE_LOGGER:
        myFile.close();
        lcd.setCursor(0,2);
        lcd.print("Loged");
        NextState = STATE_READ_FINGER;
        etat = 0;
        break;
    default:
        NextState = STATE_START;
    }
    // next loop()
    LoopState = NextState;
    delay(200);
}