Virtual machine (VM) image files are saved in such a way that thwarts deduplication, so every time you use your virtual machine the multiple-gigabyte image file is completely changed and SpiderOak is forced to upload it in its entirety. This is a limitation of the file format, and how the image file needs to work, and isn't something SpiderOak ONE or Groups can overcome or work around.
If your interest is in backing up particular user files inside the virtual machine, you can install the appropriate version of ONE or Groups inside your VM and back up the files that way, as though the VM were its own separate device. Syncing can be problematic, particularly if the virtual machine has a time offset relative to your other computers, but if all you're wanting to do is back up certain files, this should work fine so long as the VM has adequate resources for the application to do its work.
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