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Contrary to advice given here I'm not observing LOST.DIR folder created in cases of corruption. Here's my sequence of steps:

  1. Unmount external SD card in Android.
  2. Put it into external card reader for faster file transfer.
  3. Eject from external card reader. (Using "software eject" of the drive in Windows should which is equivalent to "safely remove hardware".)
  4. Put SD card back into Android phone and let it "scan media files".
  5. Directories end up read-only through Android and some files cannot be read because they're reported to be "modified or deleted".

This is sad, transferring files through my phone is very slow which is why I'd like to use my external reader for this.

It appears that Android remembers only the files that were indexed last time and rejects files added externally. Media scanning is suspiciously fast when I insert back the card.

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It sounds like your filesystem is being corrupted by whatever else you're using to write to it with the external card reader. Probably you need to be sure to unmount the device correctly before removing the card from the reader. For example, in Windows you need to select "Safely remove hardware".

When you write files to the SD card, from any kind of computer, the writes happen in the background: like when you're noting down what someone tells you, you're always a few seconds behind them. Removing the card before the write is finished is like snatching the paper away as soon as you're finished talking, before you write down the last few words. The "safely remove" operation, whatever it's called on your OS, ensures all writes are finished.

  • Edited my post to make it more clear. I meant "software eject". – m33lky Oct 21 '14 at 16:50
  • I wasn't accurate in my description. I did this one more time. It appears to be a permission problem. – m33lky Oct 27 '14 at 15:29
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Files that are put externally have different permissions from those that you put through MTP. You should use MTP or change file permissions.

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