No, you can safely import ETS projects again. We will keep all current configuration and put new information in a special place called the "Review room". The review room is a place where you can keep accessories that are not visible in HomeKit (or Amazon Alexa and Google Assistant) and decide to move to a real room later.
If you do want to overwrite all current configuration and import ETS, then go to Settings -> System and click on "Reset configuration".
Don't forget to make a backup, better safe than sorry.