Some months ago I encountered a corrupted directory. It was on the family photos USB drive (formatted as NTFS so family members can use it on Windows). I noticed when copying files in the file browser that something seemed amiss - files were just, not appearing?
Windows ironically saved the day. chkdsk
was able to fix the corrupted directory before things escalated. A full integrity (with MD5 checksums) against the copies on another drive proved the files were still good. Lucky miss!
Honestly can't remember which NTFS driver it was, but never had corruption like that before! Thanks for the tip on disabling the driver.
This might be to do with how many clusters it's formatted with.
E.g. 100 files of 1 KiB on a 4 KiB clustered disk = 100 KiB logically, 400 KiB physically.
My method of checking integrity is to generate a checksum list and verify that against the other medium:
cd /path/to/source
find . -type f -exec md5sum {} + >> /tmp/checksums.md5
cd /path/to/dest
md5sum -c /tmp/checksums.md5