Someone can probably write a script to do such a thing but I have no idea how to do that.
If you are using windows, this is what I would do:
- Open up your Documents folder (or any other folder that has the sub-folders containing your epubs).
- Using Windows Explorer, do a wildcard search for epubs. i.e. *.epub.
(This will display all the epubs in the all the folders below and including the top-most folder.)
- While holding down the Ctrl key, select all of the epubs that you want and either copy or cut and paste all to a new folder.
Clear as mud?
If you're not using windows, I can't help either.
*edit* Too slow. Wilyumm beat me to it.