This weekend I started building a media center with the CHIP and an old external hard drive which formerly functioned as my Time Machine backup (here’s the new Time Machine drive). In the process, I needed to delete the old Time Machine backup but NOT format the drive. This proved to be harder than you’d think.
Long story short, the tool you’re looking for is `tmutil`. It exists solely to modify and delete Time Machine backups. Use it like this: `sudo tmutil delete /Volumes/YourDisk/Backups.backupdb`
Source: Remove TimeMachine Backups.backupdb file manually via terminal command line | Garbage In Garbage Out : Tech Blog