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You know I don't have the experience yet Andy, but I'll at least try and help - just give it a whirl with the mixed data, can't hurt?
Can you set the colour temps with your camera? If you set it for the filter separately to the non-filter setup, it might minimise colour differences, that's what I do. Though I'm yet to combine the 2 types of data.
In anycase, you should be able to neutralise the combined colour after combining. Tell us how it goes, as I'm sure I'll be doing plenty of that in future!
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