The loss of UID 0 tends to be a host side issue, and is unlikely to be the result of encryption. For example, Linux has an extended and different permission system compared to Windows’ VFAT and NTFS, and if the image is built from a host PC that is running on one of those other filesystem types, then permissions are lost the moment the content to be added is on one of those filesystem types. Is there any chance your host PC is using a non-Linux filesystem type?
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