I recall once having an SD card with a mysterious file in the root folder with system and hidden attributes on it. I decided to delete the file and some time later (months), the card suddenly stopped working.

It maybe stopped working once the OS decided the bytes were available for use (which it would only have done without the file marking that space as unavailable) and overwrote that section. I suspect defragmenting or otherwise moving the file about for whatever reason would have had the same effect.