andy16h,
Since you haven't really received any good help from anyone other than zkflow (how you interpret what I just said is up to you
), I'll let you know what I just found out.
Since you stated you are pretty good with computer programming, you can definitely manually edit all of the .sce files. They follow a very simple format:
132 bytes of header info (with the file names, which I am guessing you don't care to change), including a break before the data.
2048 bytes of the DMX output (what should interest you).
Footer info (I haven't seen if there is anything useful here yet).
I don't know exactly what you are trying to do, but what I would probably do if I were you is whip up a rudimentary program in your language of choice to manipulate all of the scene files at once, swapping positions in the DMX universe as needed. I'd test one scene out, and see what happens in either the 3D viewer or connected to physical fixtures, then go from there.
I hope this helps!