After some hard work to fix it, I thought I got everything right but still not working. Maybe even worse.
The serial transmission now stops randomly before the python script can even finish running 
I guess I am doing something really wrong with those serial transmissions but I just can't figure out where went wrong......
Python script:
import binascii
import os
import serial
import time
ser = serial.Serial('/dev/ttyUSB0',9600)
recv = -1
counter = 0
totalcount = 0
with open('TestCard.txt', 'rb') as f:
  hexdata = binascii.hexlify(f.read())
  hexlist = map(''.join, zip(*[iter(hexdata)]*2))
f.close
while(1):
  #Wait for arduino to ask for address
  if(ser.readline()=="address\n"):
    ser.write("0")
    print "written 0 \n" #Give arduino address I wanted to write
    break
for a in hexlist:
  ser.write("srq\n")
  #Check if arduino is good to revcieve data
  while(ser.readline() != "OK\n"):
    if(ser.readline() == "write\n"):
      print "write\n"
    ser.write("srq\n")
    print "srq\n"
  while(ser.readline() != "read\n"):
    if(ser.readline() == "read\n"):
      print "sok\n"
      ser.write("SOK\n")
      break
  print "sok\n"  Â
  ser.write("SOK\n")
  #Send data
  ser.write(a.encode())
  print "written " + a.encode()
  counter = counter + 1
  totalcount = totalcount + 1
  #else:
    #while(ser.readline()!="Next Block\n" and ser.readline()!="Done\n"):
      #continue
  if(counter == 16 ):
    print "\n\n16 bytes\n\n"
    counter = 0
ser.write("EOF\n")
print "\nEOF\n"
ser.close()
Arduino sketch:
#include <Wire.h>
#include <SoftwareSerial.h>
byte buff[16];
int addr=-1;
int count=0;
char readed[5];
char srq[4] = "srq\n";
char eof[4] = "EOF\n";
char sok[4] = "SOK\n";
byte recv;
bool ended = false;
void i2c_eeprom_write_byte( int deviceaddress, unsigned int eeaddress, byte data ) {
  int rdata = data;
  Wire.beginTransmission(deviceaddress);
  Wire.write((int)(eeaddress >> 8)); // MSB
  Wire.write((int)(eeaddress & 0xFF)); // LSB
  Wire.write(rdata);
  Wire.endTransmission();
}
// WARNING: address is a page address, 6-bit end will wrap around
// also, data can be maximum of about 30 bytes, because the Wire library has a buffer of 32 bytes
void i2c_eeprom_write_page( int deviceaddress, unsigned int eeaddresspage, byte* data, byte length ) {
  Wire.beginTransmission(deviceaddress);
  Wire.write((int)(eeaddresspage >> 8)); // MSB
  Wire.write((int)(eeaddresspage & 0xFF)); // LSB
  byte c;
  for ( c = 0; c < length; c++)
    Wire.write(data[c]);
  Wire.endTransmission();
}
byte i2c_eeprom_read_byte( int deviceaddress, unsigned int eeaddress ) {
  byte rdata = 0xFF;
  Wire.beginTransmission(deviceaddress);
  Wire.write((int)(eeaddress >> 8)); // MSB
  Wire.write((int)(eeaddress & 0xFF)); // LSB
  Wire.endTransmission();
  Wire.requestFrom(deviceaddress,1);
  if (Wire.available()) rdata = Wire.read();
  return rdata;
}
// maybe let's not read more than 30 or 32 bytes at a time!
void i2c_eeprom_read_buffer( int deviceaddress, unsigned int eeaddress, byte *buffer, int length ) {
  Wire.beginTransmission(deviceaddress);
  Wire.write((int)(eeaddress >> 8)); // MSB
  Wire.write((int)(eeaddress & 0xFF)); // LSB
  Wire.endTransmission();
  Wire.requestFrom(deviceaddress,length);
  int c = 0;
  for ( c = 0; c < length; c++ )
    if (Wire.available()) buffer[c] = Wire.read();
}
void LOL(char* arr)
{
 strcpy(arr, "LOL\n");
}Â
bool checksrq(){
 bool same = false;
 for(int i=0 ; i<4; i++){
    readed[i] == srq[i] ? same = true : same = false;
  }
 return same;
}
bool checkEOF(){
 bool same = false;
 for(int i=0 ; i<4; i++){
    readed[i] == eof[i] ? same = true : same = false;
  }
 return same;
}
bool checkSOK(){
 bool same = false;
 for(int i=0 ; i<4; i++){
    readed[i] == sok[i] ? same = true : same = false;
  }
 return same;
}
void setup() {
 Wire.begin();
 Serial.begin(9600);
}
void loop() {
 // put your main code here, to run repeatedly:
   if(ended == true){
    delay(1000000);
   }
   while(addr==-1&& ended != true){
    Serial.print("address\n");
    addr = Serial.read();
    delay(500);
   }
   while(1){
     for(int i=0 ; i<4; i++){
      readed[i] = Serial.read();
     }
      if(checksrq()){
       delay(5);
       Serial.write("OK\n");
       LOL(readed);
       break;
      }else if(checkEOF()){
       ended = true;
      }
      LOL(readed);
      delay(1);
   }
   Serial.write("read\n");
   while(checkSOK == false){
    delay(1);
    Serial.write("read\n");
   }
   for(int i=0; i<16 ; i++){
    buff[i] = Serial.read();
    count++;
   }
   LOL(readed);
   if(count == 16 && ended != true){
     for(int i=0 ; i<16 ; i++){
       addr += i;
       //i2c_eeprom_read_byte(0x50,addr)!= buff[i] ? i2c_eeprom_write_byte(0x50,addr,buff[i]) :  delay(1);
       delay(5);
       Serial.write("write\n");
    }
     //i2c_eeprom_write_page(0x50, addr, buff, sizeof(buff));
     //delay(10);
     count = 0;
     Serial.write("Next Block\n");
   }
}