Sometimes if permissions were not preserved some functions will fail. One of those is sudo, and perhaps some of the login function. One reason this can happen is if the file system of the host is not a native Linux type, e.g., if you use a virtual machine and the underlying file system is NTFS, something odd like this would happen. Can you describe more about your flash host, and perhaps more details about exactly what the login failure text output is?
If you’ve tried to flash, then you won’t be able to clone the existing root partition. Flash overwrites the root partition.