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AndreaMosaic threat grayscale images as color images, working always with the three color channels RGB. So it can happen that it choose a color picture for a grayscale tile because the shape of the color picture match better the tile. What about converting manually the final mosaic into grayscale, even when it used colored tiles (except of course for the colored area of the main image).
If you want to separate strictly the grayscale tiles and colored tiles then the only solution is to make two identical mosaics using two different tile archives, one with colored tiles and the other with grayscale tiles. Then with a Photo Editor you merge manually the two mosaics, cutting out the colored mosaic parts into the grayscale mosaic.
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