virtualbox.org

Is it safe to convert .vmdk disks to .vdi for some pre-made virtualbox disks, like Whonix OS, which are based entirely on security? Is it possible converting the whonix gateway and whonix workstation disks which are in .vmdk format to .vdi to break somehow the security of the system installed on the disks?

Absolutely not. VDI, VMDK a container format. It has not a single clue of what's there in terms of files or security (metadata). It only sees block of data, sectors. And sectors do not have security associated with them. The OS that's using them does.