X86, overlay problems?

I noticed on my install that some files are present in /overlay/upper
like var/lock, var/lock, etc
but they don't appear on the actual filesystem.

How can I fix this?

Your title noted problems - what issues are you having?

On the default configuration, a tmpfs is mounted on "/var", overriding whatever contents might exist on the underlying filesystem.

Execute "mount" without parameters to confirm how is your system running.

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Nevermind, i figured it out...
I had "make var persistent" checked in my build config.
But that doesn't seem to work correctly.