My 1TB flash drive has 100s of GB of mysterious "used" data

My Mid-2014 Retina MBP has the 1TB Flash drive. The other day I noticed I was almost out of space (<20GB free), which seemed a little odd. Did some cleanup, and still had less than 100GB free.
Currently I'm seeing 83.3GB free, 840.5GB used. But all actual data that I can see totals only 470GB. This is via Get Info, DaisyDisk, OmniDiskSweeper and Disk Inventory X. There do not appear to be any invisible files that account for the additional 370GB or so of "Other". The disk is encrypted with File Vault.

ODS can't see the whole filesystem when you run it just by double-clicking; it only sees files that you have permission to read. To see everything, you have to run it as root.
Back up all data now.
Install the app in the Applications folder as usual. Quit it if it's running.
Triple-click anywhere in the line of text below on this page to select it, then copy the selected text to the Clipboard by pressing the key combination command-C.
security execute-with-privileges /A*/OmniDiskSweeper.app/*/M*/* 2>&-
Launch the built-in Terminal application in any of the following ways:
☞ Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
☞ In the Finder, select Go ▹ Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
☞ Open LaunchPad and start typing the name.
Paste into the Terminal window by pressing command-V. You'll be prompted for your login password.
The application window will open behind other open windows. When you scan a volume, the window will eventually show all files in all folders, sorted by size. It may take a few minutes for the app to finish scanning.
I don't recommend that you make a habit of doing this. Don't delete anything as root. If something needs to be deleted, make sure you know what it is and how it got there, and then delete it by other, safer, means. When in doubt, leave it alone or ask for guidance.
When you're done with the app, quit it and also quit Terminal.

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