I even deleted save data in AppData\Local\Gaijin Games\Runner2\ and disabled Steam Cloud for game, but it didn't reset my progress.

One way of doing it would be by using family sharing. Though it doesn't reset your progress on your current account it allows you to start fresh on a new account.

Create a new account and sign into it in the client.

Then sign back into your main account and enable family sharing on your main account and authorise the new account to share your games.

Sign into the new account and you can play any of your games (with a few exceptions) and the account has it's own progress and achievements.

I found a way, delete steam cloud files from main steam folder.

Originally posted by SomeGuy:

I found a way, delete steam cloud files from main steam folder.

Where are these Cloud files? I can't find them...

А где эта папка?

I know this question has been answered for a while, but I just found another way. Log out of Steam and shut down. When you restart, the Steam login popup should appear. Click cancel and go to your appdata folder. Look around until you find a folder for Bit.Trip and find the subfolder data. Inside data there should be a .txt file and your saved data. You can delete both or just the saved data, either way will work. As long as you're logged out, the cloud won't replace your data.

1. Stop the game.
   
2. On your Steam Library, right click the game, go to Properties -> Updates and disable Steam Cloud synchronization.
   
3. Go to <Steam Path>\userdata\<your user ID>\218060 and delete all content. Note that 218060 is the game ID.
   
4. Start the game. It will create new save files and your progress will be reset.
   
5. If you want to sync with Steam Cloud again, stop the game and reenable synchronization on the Steam app properties. Next time you start the game, Steam will prompt you to choose if you want to send local files to the cloud or download the previously synced files.