fdupes compare the files by they md5 checksum. If the contents of the files is different then md5 checksum will be different too and the files will not be identified as duplicates.
Easiest (and in my opinion best) solution is to use /usr/sbin/mtree. I even wrote a small tutorial on how to use it some time ago.
The file name doesn't matter. The files are compared by they size and md5 checksum.
cmp
i get
although the files are visible when I do a directory listing... They are on an NTFS partition and maybe have invalid filenames.... Must investigate further.: No such file or directory
find /path/of/the/base/directory -name Thumbs.db -delete
find /path/of/the/base/directory -name .DS_Store -delete
For example you can have two mp3 files with different bitrate of the same song. Even if the song is the same the md5 checksum of the files will be different and it won't be detected as duplicates.
If your goal is to remove similar music files then search for software that can compare they acoustic fingerprint or mp3 id3 tags.