DLMWRITE('FILENAME',M,'DLM',R,C) writes matrix M starting at offset row R, and offset column C in the file. But it will completely over-write the existing file anyway. It just leaves some delimiter to make the offset. It's not going to open the old file, find the offset and just over-write the new data.
You'll have to read in the whole data, do the proper replacement in MATLAB and then write it back.