How were the files/folders (which had missing labels) copied from old to new drive? It would need to be something which preserves NTFS ADS metadata to keep all the old labels.
With tools that can copy that metadata (including Opus), it's also often the case that metadata for folders will only be transferred if the folder is created as part of the copy process. Put another way, it won't usually be copied over for folders which already exist.
If you still have the old drive with the labels on it, the BackupMeta (Backup and restore Opus metadata) tool Lxp wrote may let you transfer things, by backing up the metadata from the old drive, then editing the backup so everything points to the new one and restoring that. That should be much quicker than copying all the actual file data again, as it'll only deal with the metadata.
Before doing anything, check that Opus sees the labels on the old drive correctly. If it doesn't, there may be some other things that need doing first with the Opus configuration, which we can go into if needed.