You know, it is hard for me to give a guarantee. There are so many different Windows extensions and so many file systems in Linux, etc.

But the simplest thing to do is (on Windows):

1) Use Windows Explorer to copy files to another physical disk (not another partition on the same disk)
2) Delete the original files
3) Copy back from the backup disk to the original place
4) Keep the backup copy made in (1), well for backup.

On unmodified Windows the above procedure will greatly reduce the number of fragments, frequently to the minimum (one per file). But the various online antivirus protection tools can completely screw this up. So at least exclude the Bitcoin directory from the online virus protection. The occasional scan only virus protection can stay.

If you really don't have a separate physical drive then at least zip the files, delete, unzip and keep the zip for backup.