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You've gotta make sure that when you recombine, you're picking the right images for the red, green and blue channels.
Until you get the hang of it, when you do a split, it's named red/green/blue, but after you do a deconvolution the names are gone. So, after each deconvolution, go Edit->Image Title, and call it something like "red-deconvolution" etc, so when you RGB combine you can find the right image for the right channel.
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