I went ahead, and fixed the issue with enabling the Ship Mesh Highlight Filter option. For those that are unaware. The Ship Mesh Highlight Filter in your Sins Options\Effects is meant to make ships "glow" the further out you zoom from them. To make them easy to see from a distance. When you replace a vanilla mesh with a mod mesh the model may, or may not have a bright glow to it in game with the feature enabled. SoA 2 had lots of problems with this, and we have struggled with this problem from day one. This is why we said Disable the Ship Mesh Highlight Filter option in the mods ReadMe. You dont have to do that anymore. Its fixed.
I stumbled on the solution pretty much by accident, and figured out how it works by experimenting. In each ship, and structure entity file there are values that read something like this.....
minShadow 0.000000
maxShadow 1.200000
NOBODY knew (that i am aware of) what those values in the entity file were for! If someone did they didnt tell me about it. I played around with changing values to see what results they produced. This is what i know so far.
minShadow is how much the unit "glows" on a constant basis with the Ship Mesh Highlight Filter feature enabled. No matter how far, or close you zoom on the unit. Some vanilla sins units have it set to 0.100000, but most of the units have it set to all zeros. Obviously the higher the number the brighter the ship "glows". This is probably used for the very small, dark, and hard to see units. This entry was very important for my tweaks to the Borg models.
maxShadow is the more important of the two. It is how far you zoom out from the ship before the ship starts "glowing". The further you zoom the brighter the glow. As with minShadow the higher the value the brighter, AND sooner the ship will start glowing when you zoom out. The example value above is from the Vasari Light Frigate. Capital ships, and structures have much lower values. Being as they are much larger units.
Basically it all depends on the size of the mesh itself, and you have to play around with the values until it looks right in game. All SoA 2 units have been tweaked so that there are no more "glowing" ships with the feature enabled when zoomed up close. However when you zoom out the mesh will start glowing just before they turn to icons. Just like the vanilla sins meshes.
EDIT: Heads up people. IC just released yet another diplomacy patch. Dunno if this one will break the mod or not. From the change notes i think it will. If you wanna keep playing the SoA 2 dont update diplomacy yet. At least till we check this out.