Yes, that’s what I thought, those dir.c9r-files are very important for the folder structure.
But it means that not all files where restored from the backup. I would recommend to check the diff between this folder in the backup and the recovered one but nice that you got to your files back 
I made a short video for you to see how messed up the briefcase is. There is folder that has the dir.c9r file and has others that do not have! Do I have to assemble one by one each folder in the structure?
Normally you don’t have to do anything in the d-folder. I can only recommend you to make sure when restoring the vault folder that all files and folders are actually restored from the backup. I can not say why these dir-files are not in your recovered folder, so I can not judge whether it is enough to rescue the dir-files or whether other files/folders will be missing too.
I also wonder how you can restore the dir-files when they were obviously not taken into account during restore.
If I were you, I would either try to compare the two folders (backup and recovered version) by machine to know what the difference is and then be sure that when I have eliminated all diffs, the vault is complete again. Or restore the vault again from the backup and make sure that all files and folders are taken into account.