There is a "directory comparison" mode build in FTP Voyager. Turned on, I see the files in different colors: green (same), red (differences) or blue (missing).
It would be a great feature - for red files (those with differences) - to compare the contents with an external comparison tool (i.e. Araxis Merge) directly within FTP Voyager. I've been using this feature for years now on Mac with a FTP Client called "yummyFTP". Unfortunately, I haven't found any FTP Client for Windows that offers this functionality.
The call to that external tool could be an option when transferring files. Now, if a file already exists, I'm asked what I'd like to do: "replace", "cancel" or "rename". Why not just put a fourth option in there called "compare"? If choosen, FTP Voyager would download the remote file to a local, temporary storage, and call the comparison tool with both files. Shouldn't be a very big thing?