Original Boot Drive will Not work after Acronis Clone to External Drive. Will only Boot external Drive now in.
Steve, you seem to be the absolute legend so hoping you can help. I have a 2 week old Windows 10 pro computer. I have been setting it up from my old Windows 7. All was well. I did a clone early on. From my internal drive which is a 2TB SSD to an exact model drive. The external was in my DVD bay. The first clone early one worked great with Acronis 2020. The next one was not working. It was stuck on preparing. I got on with Support. This woman Vicky helped me and said seems like the external needs to be reformatted. Anyway then came when she said you need to restart. I said i always clone from windows if i restart will it clone from windows. She said yes. Well it did not. It went into this sort of DOS mode and started cloning. It cloned the disk and then went to windows. I went to check it through the disk manager. Come to see Disk 0 was D drive and Disk 1 was C drive. Now i decide to reboot and take the External drive out of the bay. except it wont reboot. It goes through the blue screen of your windows ran into a problem. Even with the fix it kept cycling over and over. Then i went to bios. Looked there. Its a UFEI boot. I only saw one drive as I removed the external. It would only boot if i had the external now now with the internal. once booted it seems like both are identical but it wont boot off the internal. Support has been usless and they took my working computer and messed it up. Its like they are saying its confused on the hardware but i dont know how to fix this to boot off my internal drive. i feel helpless and had a working computer i did so much work to and now they messed it up. I am running UEFI with Windows Boot manager. It seems like it merged my internal boot sector to the external drive in my DVD bay and now wont boot without me having the external on. Repairs do not work to the internal drive. Data present but it wont boot off the drive. It goes into a blue screen cycle which it goes circular on and will not repair.

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Scott, as discussed offline from the forum, the partitions on your 2 cloned drives are correct but reflect how Windows see them with differences between the active boot system drive and the clone of the same present in the same system.
With regards to the $Windows folders, these are created by either Windows Update or by an upgrade of Windows. You can use the Windows 10 disk cleanup tool to clean these if needed.
To access the cleanup tool, right-click on your C: drive in Explorer, select Properties, then on disk cleanup, then after the initial cleanup runs, select again on the further option to cleanup system files, which will give a longer list.
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