Your files may be just getting too cumbersome. Since you have an on board clock, you can use it to name a series of files. This may fix your problem simply by having smaller files. Even if it doesn't, you may ultimately find it a better way to manage files.
You might find this code useful. I simply call it up once at midnight
#include <SD.h>
#include "RTClib.h"
#include <Wire.h>
#include <string.h>
RTC_DS1307 RTC;
char filename[] = "00000000.CSV";
File myFile;
void setup()
{
Serial.begin(9600);
Wire.begin(); //Important for RTClib.h
RTC.begin();
if (! RTC.isrunning()) {
Serial.println("RTC is NOT running!");
// following line sets the RTC to the date & time this sketch was compiled
// RTC.adjust(DateTime(__DATE__, __TIME__));
return;
}
Serial.print("Initializing SD card...");
// On the Ethernet Shield, CS is pin 4. It's set as an output by default.
// Note that even if it's not used as the CS pin, the hardware SS pin
// (10 on most Arduino boards, 53 on the Mega) must be left as an output
// or the SD library functions will not work.
pinMode(10, OUTPUT);
if (!SD.begin(4)) {
Serial.println("initialization failed!");
return;
}
Serial.println("initialization done.");
}
void loop()
{
getFileName();
createFileName();
delay(3000);
}
void getFileName(){
DateTime now = RTC.now();
filename[0] = (now.year()/1000)%10 + '0'; //To get 1st digit from year()
filename[1] = (now.year()/100)%10 + '0'; //To get 2nd digit from year()
filename[2] = (now.year()/10)%10 + '0'; //To get 3rd digit from year()
filename[3] = now.year()%10 + '0'; //To get 4th digit from year()
filename[4] = now.month()/10 + '0'; //To get 1st digit from month()
filename[5] = now.month()%10 + '0'; //To get 2nd digit from month()
filename[6] = now.day()/10 + '0'; //To get 1st digit from day()
filename[7] = now.day()%10 + '0'; //To get 2nd digit from day()
//filename[8] = filename + ".csv";
}
void createFileName(){
myFile = SD.open(filename, FILE_WRITE);
myFile.close();
}