That cannot happen, because chakras are organic in nature, not synthetic. They could make something that vaguely resembles but it's impossible for it to have the same functions. Higher abilities are precluded to synthetic things.
An AI is ultimately a programme, a series a calculations. It's not something that exists on a higher dimension like chakras, your aura and many other parts of your soul. You pull the plug and an AI stops working, whereas you cannot pull the plug on a true living being.
Also, to specify to other readers, a machine will never be able to directly damage or interfere with something like a chakra. It can interfere with weak auras, sure, and can indirectly attack the chakras by attacking related body parts, but never directly.
This type of technology is very limited from the spiritual point of view. Even if you microchip an organic body and the AI takes over, it's still impossible for it to use spiritual abilities. A less limited type of technology, which is actually the enemy's goal, involves creating something like the Greys using humans as base materials. That would be able to use some spiritual abilities, but it's completely different from AIs and much more advanced.