Not sure if there is anything set up in DW yet, it does give a status window of what files were updated, you could possibly work backwards form that list (still a bit cumbersome). I also believe that if you change the template and upload it to your server, it will prompt you as to whether or not you'd like to "include dependant files", and (in theory) it will also upload the files linked associated with it... but that may need to be tested to see how well it works on a larger site.
As a possible alternative, you could use "Server Side Includes" - which is a single file which contains a portion of your page (the top navigation, footer area, etc.), and any page that uses this element will automatically update when you upload just that one element. Here is a link which explains it better: http://www.smartwebby.com/web_site_design/server_side_includes.asp and there are several others on the web that offer more detailed explainations - one caveat is that the web server you use would need to be set up to accept SSI... most do, but something you'd need to look into beforehand...
Hope that helps,
The solution is to make a ftp queue file for FileZilla based on the logfile from the template changes.
You can use EDIT | Select recently modified files, to find those files. But the granularity is only per day, so it's not very specific, i.e., you can select files modified within the last day but not within the last hour.