As a follow-up...

I never came back to describe the process I had to go through to restore all the files back to their original locations. This was only possible because I started to restore the files shortly after they were moved to the Trash and because my harddisk had not yet been reindexed. Accessing the old index of my harddisk, I had to search for each file name individually to reveal to me what the original location was (this had to be done from Terminal). It was a very long and tedious process!