Re: Files being deleted randomly.
Sorry to say this, but that is likely to be the USB reader device.
I've had repeated failures of the same nature and they stopped when I went out and replaced the built-in card reader with a USB-plugged card reader.
Size and speed of the SD card didn't really make any difference. Encountered the errors ranging from class 2 256MB up to class 10 32 GB.
Ubuntu 15.04 Mate, Mint 17.1; MS Win 8.1, Win10 TP.
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