Several months ago, I was using Dropbox while using Fedora as my primary OS. Then, my Internet connection was disconnected for a period of several months. In the meanwhile, I reorganized my Dropbox contents i.e. moved the contents around for better organization and also removed Fedora to install Windows 7. However, now that I have Internet access and hence install Dropbox again, it appears that Dropbox is forcing me to download the old file list from the cloud, and download several files that I deleted during the time when I had no Internet access. So, how do I override the filelist on the cloud with the file list on my laptop at present?
I think in this case, you basically have to start from scratch.
I would move the files out of your Dropbox folder, then go to dropbox.com and delete all the files. Let the system sync and then copy your files back in.
I suspect that you probably set up Dropbox and told it that the location was your Dropbox folder rather than installing Dropbox clean and then copying the files in. I think that in a dispute Dropbox shows you it's before you show it yours so it will download all the files it has, then upload new ones from your system.
I don't know what the policy is if there is a file dispute, whether it's last modified or Dropbox becomes the source. I haven't had it happen yet.