I just tested this out too. Recolored the ancient oak tree purple.
I think you are missing a trick on saving it as a .qb file. When the Qubicle Binary Export Settings window comes up, you must get the settings right. If you don’t get it right, the game will not handle it.
Z-Axis: Right-handed. If you use left-handed, the tree will be reversed in game.
Color Format: RGBA. If BGRA is used, it won’t be the right colors.
Single Object: Ticked if it a single object, unticked if you are exporting multiple objects as one qb file (especially if it’s a model that will be animated).
Hollow: Unticked, but no effect that I can tell.
Compression: Game will crash on load if ticked. Absolutely cannot handle compression.
Visibility Mask: Ticked, but no effect that I can tell.