I’m just going to leave this here for anyone who runs in to this in the future (and I know you will, because I’ve seen a lot of these questions and no one seems to know the answer)
This is what I ran to manually refresh the usage and remove the enforcement. Run this in the CLI:
/usr/local/CyberCP/bin/python /usr/local/CyberCP/IncBackups/IncScheduler.py CalculateAndUpdateDiskUsage
/usr/local/CyberCP/bin/python /usr/local/CyberCP/IncBackups/IncScheduler.py checkDiskUsage
Now the disk usage show the correct values. Check if you can upload media in WP. If not, the limit enforcement is still there. Run this last command: (replace {{website}} with the folder name of the website)
chattr -R -i /home/{{website}}
I hope this helps someone in the future. I’d be great if this runs automatically on changing the package, right?