There are a few meshes that the unpacker struggles with; all you can do with them is to not attempt to convert them back and forth with DAE files but they should repack okay in their unaltered GR2 format.
I'm curious about you needing the mesh to customise the colours though: you just need to alter the relevant DDS files for that. You also don't need to repack the stuff for your WIP mod to make it show up in game, though you do need to add or update the texture definition in the modding engine with the correct path to your mod directory as it tends to use the default path by, er, default.
And this may simply be down to my own inexpertise, but don't try to create a new PBR: I've never managed to get them to work as intended. Modify or copy an existing one that is "close enough" but don't try to update its path, and just apply any new texture GUIDs to the relevant record in the modding engine instead.
