If you use Sonor (or any other sequencer with this capability), isn't there a 'batch' feature that allows you to do certain operations on a whole bunch of files at the same time?

Perhaps if it is as easy as simply removing certain sys-ex codes, and changing a particular PC#/32/00 code to a different one, maybe a script could be written to do the whole lot in one go?
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An arranger is just a tool. What matters is what you build with it..!