I this answer in the forum. It tells me how to prevent it in the future but it doesn't tell me how to fix the problem If it has already occured. I've tried manually scanning to no avail.
Copy In Progress
Another thing that can cause issues is if you’re copying content to the drive and directly into the content location. In such a situation, when the content copy first starts, the Plex Media Server scanner can note the change and then wait 60s. If nothing else has changed at that point, it will perform a library scan.
However, if your content is copying and takes longer than a minute, then it’s possible for a situation to occur where the scan occurs before the copy finishes. Subsequent scans would not actually look in the directory because it doesn’t look like the directory changed at all.