With version 1.0 and 2.0, you currently can't erase save files. If you have all four save files used, you might be thinking, "UH OH! How do I do more runs then!?", never fear, your speedrunning days aren't over.

If on Windows, do the following:

1. Bring up the Run menu (press Windows Key + R)
2. Type in "AppData" and hit enter. The AppData folder should appear.
3. Go into LocalLow\MixMorris\Super Mario 64 FPS
4. Delete savedata.bin
5. Start the game up
6. Your save files are now erased
7. Proceed to bust out more phat runs

If on macOS or Linux:

1. I don't know. I don't use these OS-es for running Mario Gun.