AOMEI Cloner can copy the Windows system partition set or a complete physical disk. A separate path copies one selected partition. It writes that object to another storage target for migration or replacement. The destination selection matters immediately because the clone operation formats or overwrites the target data.
The source scope changes with the clone mode
System Clone automatically selects the Windows-related partitions that the documented migration needs. On a typical installation, that means more than the visible C partition. Cloning C alone through Partition Clone can omit a separate boot partition and leave a destination that contains Windows files but cannot start the system.
Disk Clone asks for one source disk and one destination disk, then copies the disk layout and selected data. Partition Clone copies a single volume. A valid partition copy can therefore succeed without becoming a complete system replacement.
AOMEI Cloner leaves the source disk unchanged. That does not make a mistaken destination harmless: reversing the two selectors can overwrite the disk whose data the user meant to keep.
Intelligent and sector-by-sector modes have opposite size rules
The intelligent path copies used data rather than every unused sector. It can use a smaller destination when the required data and layout fit. Edit Partitions can keep source sizes, distribute unallocated space or accept manual size changes. The documented workflow can also expose an MBR-to-GPT or GPT-to-MBR destination conversion.
Sector by Sector Clone copies every sector and disables Edit Partitions. The destination must hold the source layout and use compatible sector geometry. Encrypted disks and filesystems outside the normal filesystem-aware path can force this handling, so a disk with little used data does not always qualify for the smaller-target route.
SSD Alignment changes destination alignment for a solid-state drive. Source and destination selection remains a separate step in the clone workflow.
A completed copy does not select the next boot device
After System Clone, the vendor recommends shutting the machine down and installing the cloned system disk internally before the first boot. Firmware may still need a new boot order and the correct legacy BIOS or UEFI mode. Repeating the clone does not correct either setting.
The destination partition style and firmware mode must agree. After AOMEI Cloner writes the selected data, the motherboard still uses its own boot order and firmware mode to start that disk.
Windows PE can expose a driver problem
Create Bootable Disk writes a Windows PE environment with AOMEI Cloner to removable media. That environment can run system, disk and partition clone jobs without starting the installed Windows system.
A storage controller can remain invisible when the Windows PE environment lacks its driver. In that case, the missing disk is a driver-visibility problem rather than evidence that AOMEI Cloner erased it. The recovery medium still needs access to both the intended source and target before a clone can begin safely.
