There are several scenarios where you would have several *.vmdks.
1. your VM has two or more disks like one for the system and one for the data.This may look like
system.vmdk
data.vmdk
In this case you can't merge those vmdks into one - you also do not want to do this.
2. your VM has only one disk and this one disk is split into several chunks.
system.vmdk
system-s001.vmdk
system-s002.vmdk
...
In this case you could merge the chunks into a single vmdk with vmware-vdiskmanager but it is not recommended to do so.
See
3. your VM has one or more snapshots
system.vmdk
system-000001.vmdk
...
In this case you must use snapshot-manager
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Do you need support with a VMFS recovery problem ? - send a message via skype "sanbarrow"
I do not support Workstation 16 at this time ...