Thankfully, if you make a huge enough mistake on your configuration/settings/upload to cause your FC to stop responding you can get it back to factory settings with the factory-reset firmware.
Download the TBS Agent at the following link:
Once you have installed the application, open it up, then hold down the button on the top of the cube (Next to the USB plug), and plug it into your computer.
Once connected click on 'Update Colibri Race' tab at the top.
In the drop down menu select 'Betaflight 3.1.7' and then click on 'Update'.
Wait for it to complete, and then you should be good to go.
If you are still having issues with your Atom behaving badly, open a ticket at https://rotorx.freshdesk.com