A simple Introduction of Boot Partition [MiniTool Wiki]
As a matter of fact, boot partition is the Windows partition that contains Windows directory (WINNT directory for Windows 2000). Most often, C drive is both system partition and boot partition. However, if multiple operating systems are installed on the same disk, the partition which contains the Windows operating system is the boot partition.
Windows can automatically recognize the boot partition and system partition, so does MiniTool Partition Wizard. Users should not delete boot partition as well as system partition under Windows. However, if they have to, they can refer to the guide Solutions to Deleting Drive C, EFI System Volume, Recovery/OEM Volume, etc.