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Are your drives NTFS? I believe you could use the command CHKNTFS with the switch /X
Curious as to why you would want to do this. It's totally unnecessary. With NTFS drives Scandisk/Chkdisk will ONLY run if there are errors on the drive. And if there are errors, then you need to fix them. As long as your drives remain error free then you'll never see Scandisk run.
Anyways....here:
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C:\>chkntfs /?
Displays or modifies the checking of disk at boot time.
CHKNTFS volume [...]
CHKNTFS /D
CHKNTFS /T[:time]
CHKNTFS /X volume [...]
CHKNTFS /C volume [...] volume - Specifies the drive letter (followed by a colon), mount point, or volume name. /D - Restores the machine to the default behavior; all drives are checked at boot time and chkdsk is run on those that are dirty. /T:time - Changes the AUTOCHK initiation count down time to the specified amount of time in seconds. If time is not specified, displays the current setting. /X - Excludes a drive from the default boot-time check. Excluded drives are not accumulated between command invocations. /C - Schedules a drive to be checked at boot time; chkdsk will run if the drive is dirty.
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