if you choose to start from scratch, then yes. You can however use the included save files to start at a point closer to where you were. Check the readme for details.
"Issues may arise when using save files from previous versions of this game. For the best experience, please either start the game from the beginning or use the included save files to start at the point of the story you want to play."
All I am asking is that you post the info in the Readme before the changelog somewhere more visible (as most people redownloading a game are unlikely to think they will need to read it again).
The Readme is in the root of the game’s folder and the file is in all caps to make it stand out. The line about using previous saves is the first sentence you see when the file is opened. I have also mentioned that previous saves won’t work on a number of my weekly updates.