When you issue the convert driveltr: /FS:NTFS command, at the next boot, the FAT partition specified will be converted to NTFS. NT knows to perform the action by checking the BootExecute key at boot time. The key's normal contents, autocheck autochk * is replaced by autoconv \DosDevices\driveltr: /FS:NTFS. To stop the conversion, set the key to its normal string value.

Hive: HKEY_LOCAL_MACHINE
Key: SYSTEM\CurrentControlSet\Control\Session Manager
Name: BootExecute
Type: REG_MULTI_SZ
Value: autocheck autochk * normal setting

Background information: Registry Construction Steps