I have compared the content of the smaller vdmk file (Flawless Server.vmdk) and noticed that there is an additional row in the new one.
ddb.thinProvisioned = "1"
The previous vmdk file did not had such row. Its most likely caused by the command that I have used for the initial file copy:
vmkfstools -i "/vmfs/volumes/source_datastore/Some VM/Some VM.vmdk" -d thin "/vmfs/volumes/destination_datastore/Some VM/Some VM.vmdk"
Should I try to delete it or move files again without the thin parameter?