Those two folders should be kept in sync automatically by the Dropbox syncing feature. So I don't understand why syncing would screw up the versions in your Documents folder since they should be the same as the ones in your Dropbox folder. What are the names of your Highlight files? And do you have any aliases to them pointing somewhere else?
It should stay in sync, but for some reason didn't. After those few incidents no more problems. I don't use aliases. Name of the highlighter file is Studies.hlt