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.