Can't you just break the file into seperate parts? I do it all the time. If you know the line number you'd like to start on, it really isn't that tough.
WinCNC has a Restart function. If I stop cutting during a file, I can click the Restart button and it will show me the line I stopped on. I can choose that line or give it a line number. I usually back it up a little for the restart. Example: it stops on line 1000, I restart on about line 980. It gives a smooth lead-in to the rest of the file.