In WHM, list accounts option shows all the domains disk used as 0 MB. In cpanel the disk usage is showing wrongly.

If /scripts/fixquotas and /scripts/fixeverything does not fix the issue try the below given solution.

Solution :

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WHM >> Tweak Settings >> Check the option Disable Disk Quota display caching(whm will cache disk usage which may result in the display of disk quotas being up to 15 minutes behind the actual disk usage. Disabling this may result in a large performace degradation.)
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This will fix the issue.