"Refresh one flat file" will overwrite your existing flat file (entirely, all of its contents) in your cloud drive, every time your job runs (hourly, daily, weekly, etc.).
Example: mydata.csv
"Create new flat files" will create a new file with the time-date-stamp in its name, every job run (daily, weekly) but it will not overwrite or modify the existing flat file (created an hour ago, yesterday or a week ago in a previous job run).
Example:
mydata 2022-09-06 17-17-10 YOURTIMEZONE.csv
mydata 2022-09-07 17-17-10 YOURTIMEZONE.csv
mydata 2022-09-08 17-17-10 YOURTIMEZONE.csv
Pro tip: If you want to preserve calculations or custom views on your flat file, use a tool designed to make that customization easy and powerful. Most are available for free:
Power BI
Tableau
Google Data Studio