Yes, Dropbox knows which files are newer and only syncs newer -> older. If it didn't work this way and you had 2 or more devices sharing the same account then you'd have a constant battle going on with one device pushing updated files, the other device seeing the change and pushing it's outdated files, and so on until the end of time.
There seems to be some disconnect/misunderstanding that is clouding the waters. The files aren't going to be missing on the restored Mac, they're just going to be older than what exists on Dropbox. The OP was concerned that Dropbox wasn't smart enough to know which files to keep/update.