By default, we run a script which generates colours for a number of different pieces of metadata (clade_membership, country, division, emerging_lineage, location, pango_lineage, recency, region). This script reflects a specific ordering of values, which we define in defaults/color_ordering.tsv. That ordering includes the pango lineages in your message.
You can define a custom mapping of metadata to colours as per your color.tsv, however you have to include this in your builds.yaml such as
files:
colors: my_profiles/md_color/colors.tsv
Please note that this will result in all the other custom colours generated by the above script are no longer used, and auspice will use a generic colour scale for these instead, which means that the ordering won’t be as nice! It will also mean that all pango lineages apart from the ones you define are grey.
If you want to keep our ncov-specific colours, but simply change the hex values for a few pango lineages, the easiest may be to write a small script to modify the dataset JSON to redefine them there.