I encountered the weirdest problems when hard-copying (byte-by-byte, using a disk imaging utility) a Windows 10 OS hard drive to a backup, and then booting from the backup to test that all was working. Example problems included (to the best of my recollection - it was a year ago, and just finding time to post now...) being unable to properly run an Administrator level CMD Prompt, an SQL-based program (ACT CRM) not working in odd ways, etc.
I spent a full day trying to figure out what was wrong, using different drives, different imaging techniques, etc. - all to no avail. Then, I finally discovered that the source drive had a hardware Sector size of 512 bytes, and that if the target drive similarly had a hardware Sector size of 512 bytes, all was fine, but if target drive had a hardware Sector size of 4096, wacky problems presented themselves on diverse fronts. (To the best of my recollection I could not, in that state, even run Chkdsk/r - though doubt it would have helped regardless...)
Now, before continuing, I would like to clear up the confusion between the software "Allocation Unit Size" (sometimes called "Cluster" — an integer multiple of the Sector size) settable during (for example) Windows Format, and the hardware Sector size which is not changeable. (And in case you believe there is no "hardware" Sector size (as various Amazon responders to my question regarding Sector size of specific drive models stated, sometimes insultingly :-), please see the diverse technical reference docs indicating that is not the case, including:
Fortunately, some Amazon responders did know what they were talking about. Their information, combined with my own testing, allowed me to determine which drives had 512 byte Sectors and which 4096 ones, thus allowing my to solve my problem and backup my server!
I offer the below in case it proves of use to others in the same position. (If it does help you, please let me know. I am curious as to whether the significant time to post these tech-tidbits is worth it...)