Electronic – Help understanding table in SAM E54 Datasheet

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.

The PIC18F47J53 doesn't have EEPROM memory.

As for Flash programming, I don't believe there's a simpler way to write to it than the one you tried. You just have to be careful not to write/erase an already used memory section.