You will need a downtime some time when the vmsd is invalid.
To keep the downtime as short as possible you can use vmkfstools -i to consolidate all but the very last snapshot.
Then you still need about 3 minutes of downtime to prepare the final step that gets rid of the last snapshot.
Merging the last snapshot into the new basedisk that you created with vmkfstools -i then again can be done while the VM is running.
I can give you detailed instructions when you post details (file-listing, vmware.logs ...)