#How can HA "run" yet have no files in config folder?

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woeful kettle
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I "lost" everything twice today, at various times finding no configuration.yaml, no automations.yaml, no templates.yaml that can be opened from the File Editor.

When I open terminal and go into the config folder, there are 0 files, yet there ARE files and folders at the root level.

When I go into the Automations UI screen, I see automations there. I can open them in YAML editor and see them.

How is it that I actually have an interface and am able to get into load the Settings | Automations and see them listed and in YAML if there no files present in either the File Editor or the Terminal?

Developer Tools Check Configuration says everything is OK
If I restart HA, they don't come back.
I can run a restore from a backup this morning and they don't come back.

Then, I shutdown and restart the VM and everything is fine. This acts like it is a problem at the HAOS level where the entire file system becomes inaccessible yet is still there to run the code