This article explains how to handle properly the cloned preseed volumes.
One possible solution is to use vmkfstools to manually increase the size of the smaller preseed disk: https://www.vmware.com/support/developer/vcli/vcli41/doc/reference/vmkfstools.html
The size of the preseed must match the size of the source before one can select it to be used as preseed.
- Create a place holder VM with no disks or Operating System or anything on it
- Attach the preseed disk to that VM
- Increase the size of the disk to match the size of the source
- Remove the preseed disk from the VM
- Delete the place holder VM
- Use the disk for preseeding