I'm trying to merge a couple of GeoTiff maps using Raster > Miscellaneous > Merge but the merge is only coming out in grayscale. The geotifs are using palettes color. How do I get the merge to keep the color information?
You have to expand the GeoTiffs to RGBA. Each of your GeoTiffs has a different palette, and GDAL (working in the background of QGIS) can not merge and repalette in one step.
Raster -> Convert -> PCT to RGB or
gdal_translate -expand RGBA.