1. Disable Steam cloud saves.
Right Kindred Spirits in your library > Properties > Uncheck cloud saves

2. Delete save files
You must delete the save files in both of these locations before launching the game again.
C:\Users\[User]\AppData\Roaming\MangaGamer\Kindred Spirits Full Chorus
C:\Program Files (x86)\Steam\steamapps\common\Kindred Spirits on the Roof\game\saves
"persistence" is the file you need to delete in both of these locations as this is the file responsible for planner progress, but you won't be needing your old saves if you intend on starting over from scratch so I'd just delete everything.

3. Relaunch the game from the .exe
Can be found in C:\Program Files (x86)\Steam\steamapps\common\Kindred Spirits on the Roof

4. You're all set!