Files moved partially and the rest gone!
Before you transfer any more files or make any changes to either hard drive, run Disk Utility and repair the two disks.

Hopefully, that will recover your lost files. If not you could try a commercial product like DiskWarrior, Drive Genius, or Data Rescue.

Unless you do a destructive delete, files are never actually deleted and as long as you don't save anything else to the disks the files are still there and have not been overwritten. As a last resort a data recovery service could possibly resurrect your files.