If you use the -append option, save will not overwrite any of your existing data. It will simply add the new data into the existing file. This can/will duplicate variables and structures already stored in the file.
If you want to change some of the values and not others, you should open the file and load the existing data. Then change the values you want to change in the imported data before overwriting the old file with the modified data. This is faster than appending an existing file and you don't get duplicate entries.
If you have the full data set in memory that you wish to save, simply overwrite the existing file with the data in memory. This would be the fastest way if it is possible in your code.