I've had a number of problems with CE lately that look like they'll be difficult to fix. Not sure I'll have a better experience with a different platform, but I figure it's about time to try. If nothing else, I'll have some backup copies of my VMs, which is not an obvious thing in CE.
So, here's what I've had to go through to export VMs:
Log into a CVM and then "acli" to find the vmdisk_uuid. Do a "vm.get [vm name] include_vmdisk_paths=1" to see a list of parameters. Copy the vmdisk_uuid from about the middle of the output. Exit the acli.
Run this:
qemu-img convert -c nfs://127.0.0.1/PrismCentral-CTR/.acropolis/vmdisk/[vmdisk_uuid from the previous step] -O qcow2 ./data/stargate-storage/disks/drive-scsi0-0-0-1/NameOfVM.qcow2
This command might be different depending on your setup. I'm running PrismCentral so I had to use this location to find the disk. The path is listed above the uuid in the acli command. The output target will need to be adjusted depending on your space requirements. If you leave out the target destination I believe it will save it in your current directory. That might be ok or it might be too small for the VM. I checked mine and decided to save it to the slow tier disk. Depending on the disk size it might take a very long time.
Once it completes you can use SCP (not SFTP) to copy the file off. I used WinSCP to connect to the same CVM. The path for the above command is /home/nutanix/data/stargate-storage/disks/drive-scsi0-0-0-1. The disk copy is in there for me and I can SCP it to somewhere else. I tried sending it directly to an NFS share I have running on the network but it failed permissions, despite being whitelisted. This process is cumbersome, but it works. I'm sure there are better ways...