This doesn't happen when using Zotero as recommended.

- Is there something I can do to get those documents back into Zotero?

Not automatically. You can, of course, re-add them manually.

- Is there a clean way to ask Zotero to "re-scan" the data directory location?

No.

- My custom directory location is inside a folder which is synchronized through a cloud service similar to dropbox (namely https://www.copy.com/)

I imagine this is the cause of your woes. Your data directory contains your sqlite database. This should not be opened in more than one location and it is difficult for file syncing programs (such as dropbox or copy) to treat that file properly, particularly when it is open. I suspect that copy.com synced an older version of your database to your computer, over-writing changes that Zotero had made that had the working file links. It could have been worse--syncing like this can also cause corruption. You should set your data directory to a local directory that will not be over-written or accessed by some remote tool. You can then use the Zotero Sync Server to keep your metadata/database synced across multiple computers.


You can choose to use Zotero or WebDAV to keep files synced. You may be able to do it with a third party tool (I know nothing about copy.com in particular) as long as that tool allows you to configure it to sync to just the file storage directory.

Note that this isn't something that Zotero does to make you pay; it's just a byproduct of using an unsuitable way of syncing data.
While Zotero Storage does provided the smoothest overall experience, there are a number of ways to use 3rd party service to sync Zotero attachments for free, including the options noksagt mentions in his last paragraph.

@adamsmith : thanks for the clarification.

I very much appreciate that Zotero is not trying to force the use of one it's byproducts for sync purposes (which is the reason I originally moved away from Mendeley).