In general, it's possible to update the remote file only partially, but not in your case.
What would work: 1) track the file change using a filesystem filter driver, which gives you information about what parts of the file have been updated. 2) use the protocol which allows partial upload or remote modification of the file (eg. SFTP).
As for your scenario:
Step 1 is not possible with FileSystemWatcher. Step 2 is not possible with FTP protocol which doesn't support modification of file blocks.