Moving between two databases

I just had the strangest thing happening to me. I have decided to split a large database (6Gb out of 15Gb). When transferring the data, I lost all of my true documents i.e. I see the titles of each but they are all at 0k.

Here is what I did:
Drag and drop the folder structure I was interested in between D1 and D2
Do an save/repair and optimize on each databases
On the new D2, this process gives me thousands of “orphelin” files which was strange but I deleted them all since my folder structure look right.
Redo a save/repair and optimize on D2 and close D2.
Next time around, all my true documents are gone as per the definition above…?

Which version/edition do you use? And where are the databases located? On a disk image? Is there enough disk space?