It's most likely not an issue with the replaced file, but with another .vmdk file.
To find out which of the files has/have issues, please extract the metadata from these files.
To do this, download dsfok.zip from http://faq.sanbarrow.com/index.php?action=artikel&cat=47&id=111&artlang=en, extract the executables, run the below mentioned command in the VM's folder, then compress/zip all the "xxx-....bin" files and attach them to a reply post
for %i in (*-s???.vmdk) do @dsfo.exe "%i" 0 1536 "xxx-%~ni.bin"
To make live easier, and reduce the search time for me, please start the following cloning commands, and let me know which of them throws the mentioned error.
vmware-vdiskmanager -r mdServer-000006.vmdk -t 1 mdServer-Clone6.vmdk
vmware-vdiskmanager -r mdServer-000003.vmdk -t 1 mdServer-Clone3.vmdk
vmware-vdiskmanager -r mdServer-000001.vmdk -t 1 mdServer-Clone1.vmdk
vmware-vdiskmanager -r mdServer-000007.vmdk -t 1 mdServer-Clone7.vmdk
vmware-vdiskmanager -r mdServer-000002.vmdk -t 1 mdServer-Clone2.vmdk
André