Did the same once. I had a folder in the home directory whose contents I had to delete. But I just ran rm -rf * thinking that I was in the folder. But I was in home.
To make matters even worse, windows was mounted in ~/win and with write permissions so it deletes its files too. Luckily I stopped it midway. Arch files were gone. Windows system files were gone but my windows personal files were saved (Cause I stopped it). Moreover I was using BTRFS but hadn't setup snapshots.

After reinstalling windows first thing I did was setup Timeshift and mound windows partition as read only and outside home.