Just thought I would try editing the size of the VMDK files attached to the vCenter Server Appliance VM but the Provisioned Size box is greyed out in Edit Settings.
How about this for a plan:
Add a new larger VMDK
Copy over the files currently mounted in /storage/db
Edit fstab to mount the new VMDK as /storage/db on startup and then reboot the vCenter Server Appliance.
Is there any reason why that might not work?