While cloaking is active and the mothership reaches 0 energy from draining or an emp, your cloaking will turn off but the ability still registers it as on and is unable to be used again. The cloaking button registers it as on (while not actually working) and requires you to turn it off before you can reactivate the ability. But, since you never hit the button to de-cloak, the game still thinks it's on while not cloaking

Hopefully not an intentional feature as much as I love only using my mothership for vortexing and eating up shots for my army

this was already reported, next time browse the forum first, and welcome to forums, and I don't know if this bug can be fixed since it was already brought up and nothing was done

it's worth noting since this is after the patch and the previously reported bug still exists. I'm certain this probably exists with Phoenix eye as well. Thanks for the note Raiz!