Writing/Flashing a new tune file can only ever be done after having already successfully READ your ECU's Original tune file.

Be sure that you battery is healthy and fully charged before proceeding with programming. Ensure that you are in a safe place when programming your ECU, and that you have tools and options to assist you in the event something goes a-miss.

You can flash between tune file, to tune file, to OEM (stock), etc. You do not need to flash back to OEM before moving on to each new map.