In the file menu of the Flirc GUI there is a few menu options:
When programming your Flirc, every time you program a key it immediately gets saved to flirc.
Using the "Save configuration" menu option saves in information stored on flirc in a file on your computer.
For example: this may be useful if you wanted to back up your configuration or if we need to troubleshoot a problem with your flirc.
This option applies a saved configuration file (see above) to the Flirc device that is connected.
For example: this may be useful if you wanted to program multiple flircs to work with the same remote.
This option deletes all the keys that have previously been paired with, effectively resetting the Flirc. (If you want to only one key see here)