We are aware of an issue that can cause the loot chest in the level 95 Elite Phantom base to show as empty. This is only a graphical issue, the correct number of parts has been awarded to your account. You can double check by making note of how many parts you have before and after destroying the base.
Our team is working on making sure that the correct number of parts appears in the loot chest as well so it will be clearer. We appreciate your patience in the meantime