If you've had issues updating Windows 10 after a drive clone, it's probably time to clean install.
Since I've had this issue myself recently, I'm probably not the only one to experience it. Upon delivery of my new Dell Inspiron 15 7559 the first thing I did was pop in an extra stick of RAM and install an m.2 SSD in the vacant slot. This laptop is generally superb but can suffer from some serious slow downs thanks to the slow 5200rpm HDD installed as standard equipment.
I was able to easily upgrade the RAM and HDD and install an SSD, but issues presented around the time the Windows 10 Anniversary Update dropped. Here's what went wrong and why I recommend doing a clean install over a clone.
Everything seemed to work just fine. Windows 10 was on the new SSD, everything was booting very fast, no drama. That is, until I tried to install a Windows Update. Every time the update would download, reboot to install and nothing happened. The laptop just booted straight back to Windows. No error messages, nothing. Just as though I'd turned it on for the first time.
In the end, resetting the laptop resulted in an endless boot loop and so it came to pass that a clean install was required. Upon completion and booting, being presented with a choice of drive to boot from sounded alarm bells, and then it became clear what had happened.
During the cloning process the partitions had become a total mess. The formatting of the HDD now destined to be mass storage hadn't cleared the drive properly (which was probably my fault) but as I discovered during the install process, the SSD had too many partitions for Windows on it. Best guess is that the laptop didn't know where to install Windows updates or something like that.
So, the conclusion is pretty simple. Even though cloning is quick and easy, with a lot of very user friendly software, a clean install of Windows 10 on any new drive is going to give you the best, most reliable results.