Just delete it!
In fact you can delete *all* the directories except 'filedir/'.
Howard, can you explain more?
What do you mean by "*all* the directories"?
If you are migrating, the only file you *need* is /path/to/moodledata/filedir.
All the rest are things like temp files and the, caches, trash files and so on. They will be recreated automagically.
The only exception is if you have set up a repository of some sort in there. You may need to keep that.
What about
\moodledata\lang
if you have any custom language strings?