It will overwrite, so ideally you send the second tuned ECU back to tuner to reflash with the new updates + your mods. While that is happening your stock ECU is in your car so it's operational for the few days your tuned ECU is traveling.When the ECU is flash tuned, how does this effect future Lotus ECU updates??? Could a Lotus update over write/change the tune????
Or you just don't update your ECU, or you have some way to reflash your ECU remotely but ideally the tuner gets a hold a fresh base ECU with the Lotus changes and then offers the updated in whatever method.
My Alfa 4C ECU from EC did a few rounds this way and I just used my stock ECU in the meantime.

