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After comparing 2 files through FTP, i edited 1 file.
While i opend the file for editing, ExamDiff downloads the file to my local file system, after editing when i save the file it saves the file somewhere local in the cache.
But how can i save the file directly back to the FTP destination?

You cannot save a remote file in ExamDiff Pro. FTP plug-in provides read-only comparison.

Is this something which will be build in with future updates?

Perhaps in a future version but definitely not in 6.0.