External Hard Drive folder re-structure after failure

I guess this is and isn't directly linked to FCPX but over the christmas period, one of my Hard drives became corrupt. I had stored a lot of extra client footage, photoshop files, images from stock etc here under a very neat folder structure.

I was able to restore the files I lost BUT they have all come back in one folder (note to self: Start thinking about better naming conventions for future use!) and I have 16,000 files to reorganise!!

Before I try and start a lengthy and impossible mission, has anybody gone through this? any ideas to resolve?

PS I used stella pheonix to recover the data

PPS 2nd Note to self, Make a backup of external drives too!