I had an Acer desktop with three partitions – a factory recovery partition, Windows “System Reserved”, and the main Windows OS. I didn’t want to clone the recovery partition because it took up ~20GB of space.
Using Clonezilla, I cloned only the two Windows partitions. The result: a black screen when attempting to boot from the newly-cloned SSD. No amount of finagling with drive letters, setting the partitions to active, repairing and recreating the BCD/boot sector/MBR, or Windows System Repair did anything.
Instead, I wiped the SSD and started installing a new copy of Windows 10. Once the installer tried to reboot the machine for the first time (when booted from the USB installer), I shut the machine off, booted into Clonezilla, and cloned/copied only the main c: partition from the old hard drive. This left the new System Reserved partition alone. The machine now boots normally. The trick is getting that System Reserved partition, which boots the OS, set up properly, and by letting the Windows installer do that, it’s guaranteed to work.