After some investigation, I understand the cause of this...
Unfortunately, any colors lost from this update can't be automatically recovered :'( .Dino colors, after their randomized selection, are saved to the creature and referenced by an index number only that is associated with a master array of colors. (No we can't change this unless you want your servers to slow to a crawl, string comparisons are resource expensive)
Unofficial servers that run mods are vulnerable to this issue, any change to the order of mods or anything that alters the contents of that array can cause the index to suddenly match up with a different color. It can happen at any time to any unofficial server (This last update had a pretty important change to the way mods merge color definitions to cut down on some bloated data, and that caused the issue this time)
However, I do recognize how much time everyone puts into breeding and hunting for their choice colors, and while we can't recover the lost colors, I am investigating methods for us to make it so that you can recover them in the future if this happens on your servers. I can't make any promises right now, I'm still in the investigation phase and we also have some larger bugs on our plate, the damage is also already done in this case.
Now while we can't automatically recover your lost colors it is possible for your server admins to do it manually, but don't be too hard on them if they choose not to do this, it will be very tedious and it's not their fault it happened either. There are admin commands for manually assigning colors to specific dino regions, and if you can identify what colors you had (possibly cross-referencing from the wiki, or if special mod colors you might have to ask the mod author for help) then a server admin can help you reapply the colors manually.