Electronic – How to repeatedly read and write a SMD EEPROM without unsoldering it each time

Two things come to my mind:

First, according to the data sheet, a erase-write-cycle takes at least 0.8ms, and up to 2.6ms. You say that you have an interrupt every 1ms, which may lead to a write operation. I have seen in the code that you disable interrupts for parts of the erase and for parts of the write function. But you still might get funny interleaving of the function calls. Maybe it helps when you disable interrupts for the whole sequence of erase and write?

Second - you might want to write while to power goes down, and the EEPROM write happens exactly in the moment when the supply voltage goes below the operating voltage. You can try to monitor the supply voltage, and refuse a write when it is below, lets say, 4.5V. This assumes that it stays long enough above 2.7V as the minimal operating voltage, and brown-out-detection is set to trigger only below that point.

The technique I normally use is to prefix the data with a 4-byte rolling sequence number where the largest number represents the lastest / current value. In the case of storing 2 bytes of actual data that would give 6 bytes total and then I form into a circular queue arrangement so for 128 bytes of EEPROM it would contain 21 entries and increase endurance 21 times.

Then when booting the largest sequence number can be used to determine both the next sequence number to be used and the current tail of the queue. The following C pseudo-code demonstrates, this assumes that upon initial programming the EEPROM area has been erased to values of 0xFF so I ignore a sequence number of 0xFFFF:

struct
{
  uint32_t sequence_no;
  uint16_t my_data;
} QUEUE_ENTRY;

#define EEPROM_SIZE 128
#define QUEUE_ENTRIES (EEPROM_SIZE / sizeof(QUEUE_ENTRY))

uint32_t last_sequence_no;
uint8_t queue_tail;
uint16_t current_value;

// Called at startup
void load_queue()
{
  int i;

  last_sequence_no = 0;
  queue_tail = 0;
  current_value = 0;
  for (i=0; i < QUEUE_ENTRIES; i++)
  {
    // Following assumes you've written a function where the parameters
    // are address, pointer to data, bytes to read
    read_EEPROM(i * sizeof(QUEUE_ENTRY), &QUEUE_ENTRY, sizeof(QUEUE_ENTRY));
    if ((QUEUE_ENTRY.sequence_no > last_sequence_no) && (QUEUE_ENTRY.sequence_no != 0xFFFF))
    {
      queue_tail = i;
      last_sequence_no = QUEUE_ENTRY.sequence_no;
      current_value = QUEUE_ENTRY.my_data;
    }
  }
}

void write_value(uint16_t v)
{
  queue_tail++;
  if (queue_tail >= QUEUE_ENTRIES)
    queue_tail = 0;
  last_sequence_no++;
  QUEUE_ENTRY.sequence_no = last_sequence_no;
  QUEUE_ENTRY.my_data = v;
  // Following assumes you've written a function where the parameters
  // are address, pointer to data, bytes to write
  write_EEPROM(queue_tail * sizeof(QUEUE_ENTRY), &QUEUE_ENTRY, sizeof(QUEUE_ENTRY));
  current_value = v;
}

For a smaller EEPROM a 3-byte sequence would be more efficient, although would require a bit of bit slicing instead of using standard data types.