@lucamathuse From the metadata you posted, I do not see evidence that Partclone skipped the Windows partition.
d1.partitions shows p3 as the large Microsoft basic data partition, d1.original.fstypes shows p3 as ntfs, and d1p3.img.000 exists. That indicates the Windows partition was captured. That, by itself, does not prove that the deployed content is valid, but it does not support the claim that C:\ was simply left out.
So I think it is important to distinguish between these two cases:
- The Windows partition was not restored at all
- The Windows partition was restored, but the system is not bootable
Based on what you posted, this looks closer to the second case.
The reported behaviour also points more toward a Windows boot configuration issue than a Partclone omission. In particular, the manual changes you described on the Windows side — disabling WinRE, deleting/extending partitions, and editing BCD-related settings before capture — are much more likely to produce a recovery-only boot state than Partclone “skipping C:”.
If you want to prove that C is actually not being deployed, the correct test would be a debug deploy or checking the failed target from recovery/WinPE:
- confirm partition 3 exists
- confirm it is NTFS
- confirm
C:\Windows is present
If those are present, then the problem is not that Partclone omitted C:, but that Windows cannot boot from the restored layout.