I found that if you create a new project - you can call it sample and save it to Dropbox, then you edit your list of projects and manually move them to Dropbox that works. I have done that and checked a few times and it is now working correctly. All files are syncing as they should.
If I am following things correctly, the user synced his iPad at the very beginning of this process he has recounted, but he did not sync the windows machine version.
This would account for the indexing issues. It strikes me that the other projects don’t matter because they are separate projects. So it doesn’t matter if they sync or don’t. “caravan story” was out of sync on both devices.
If I follow, syncing the windows machine would have averted the issue.