Comment 3 for bug 700734

Yes, we'd have to keep the info in both formats, but how would we write that to disk? it would only introduce more problems than it solves. The GUI has a workaround for this too: it keeps a copy of the original palette around and applies the accumulated hue shift from there in 1 single step if the hue is modified several times in succession.

I assume you're using the same workaround for your script.