If you do, during the boss fight with Namir, your augmentations will be disabled. The cutscene before will show Zhao turn them off. Afterwards, Megan will fix you up though. If you don't take the new biochip, you'll have all of your augmentations working for said boss fight. If there was higher fidelity in the cutscenes, the look on Zhao's face would be priceless when Adam remains unscathed.