I created a live LMDE5 system on a USB pen drive using Rufus and everything was working fine except for a large number of warnings and critical error messages I got from dmesg. There where some security warnings regarding a CPU vulnerability and many ACPI-related errors which appear to be related to some toxic Microsoft hardware driver politics. But among them, there was also a message

There are differences between boot sector and its backup.
This is mostly harmless. Differences: (offset:original/backup)
<...long list of entries...>
1) Copy original to backup
2) Copy backup to original
3) No action

with roughly 30-40 lines of entries. If I remember correctly, Linux systems create a working boot sector at the beginning of a disk as well as a backup copy at the end of the disk. After reading the few discussions I could find on this somewhat elusive error, I decided to choose the option of replacing the original with its backup.

Unfortunately, this appears to have been a grave mistake as I'm now getting a

Invalid system disk. Replace disk and strike any key

and the system won't boot. Question:

  • What exactly causes such a high number of offsets within the boot sector, especially on a virtually plain-vanilla installation, and what would have been the correct action?
  • How can it possibly be, if not for a serious bug, that restoring a proper, system-generated backup - following a system message asserting This is mostly harmless - bricks the system?
  • Most importantly: How to solve this issue so the system will boot again?

Note: I did not get any error referring to a "dirty bit" that appears to get set when a drive is not properly unmounted as discussed here. Also, the USB drive itself is virtually new.



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