The cloud files need to be located within the Dropbox structure in order to sync, and the folder organization is not maintained as rekordbox doesn't care how it's organized since the intention is not to browse the contents of the folders, but rather to find your music in the collection through other means.
My recommendation is as follows:
- Start by putting the files back to your local storage; they should return to the original directory.
- Move any songs you want to have in the cloud into your Dropbox folder through your Finder. This can keep the existing folder structure you have for your music.
- Relocate the songs from within rekordbox to it knows they're a the new location within Dropbox.
- Right-click on those files and upload them to the cloud. When it asks if you want to move or copy, it doesn't matter what you choose since it will find they're already in the Dropbox folder and doesn't do anything to them. The location within rekordbox will be updated to show Dropbox.