Found this to be an issue as well. Has happened 2x. I didn't reboot my iMac, but here what I did do as a work around.
Unmounted PP, disconnect HDD from PP.
Connected HDD directly to the iMac, mounted the drive.
Started Disk Utility, ran verify and repair.
*Drive reported no problems though.
Verified files were present and read/writable.
Reconnected PP and launched PP.
Each time files and folders disappeared, I was presented with a "-36" fail (the full message I don't recall), and I'm not sure what that is, except maybe it has something to do with read/write. Hope this helps. Good luck!
I'm not who I think I am and I'm not who you think I am, but I am who I think you think I am.

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