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There are some people suggested to edit the registry but the proper way to disable CHKDSK from starting up is using the /x switch on chkntfs command in command prompt. The /x switch will exclude a drive from the default boot-time check. If you have drive C: as your hard drive, then the command to disable chkdsk from scanning C: drive would be:
chkntfs /x c:
If you have 2 drive, C and D, you can disable chkdsk with the command below
chkntfs /x c: d:
Read More: Disable or Stop Auto CHKDSK During Windows Startup |