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Remove TimeMachine Backups.backupdb file manually via terminal command line

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