Can you post the code you are using? The suggestions we can give you will depend on the approach you are currently taking.
I am going to guess that you are using the "Write To Spreadsheet File.vi" in the File I/O palette. I strongly suggest you don't use that inside a while loop. If you open the multiple VIs inside this VI you will see that you are opening and closing the file every time. You can go to the lowest level subVI (Write Spreadsheet String.vi), copy that and use that as a starting point, leaving the opening and closing outside your while loop. You will see that there is a "Set File Position" function that it is set to go to the end of the file when the append to file is set to true. You could do some calculations based on your file size and the size of your last line to set the file position to always be the last line so it gets overwritten every time.
Good luck,
Fab