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The real answer is actually the same in both cases: the bits (atoms) get used for something else. Although bones can linger for quite a while, not sure if there's a file parallel for that.

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Sure there's a parallel. The bits are still there, in the same place and same order, just there's no longer an index to find and use them, so they're not "alive".

And they remain in the same place until the file space they occupy is reclaimed by the OS and rewritten with new content.

The most funny thing happens with SSDs. Even when same block is reclaimed and overwritten by OS, it very rarely overwrites the bits in NAND flash, due to the wear leveling implemented in SSD controller chip. When the actual bits are destroyed is unpredictable, probably that's why some vendors have hardware encryption there.

There is a issue with sd cards that they can revert back to an earlier state.

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