Wizkids Rules!

Phlox - During the Activation Phase, you may disable this card to remove all Disable Upgrade Tokens from all of your other [crew] upgrades.
Li Nalas - You may disable Li Nalas to prevent 1 of your (crew) upgrades or Captain Card from being disabled this round.

Can I use Phlox, disable Li Nalas instead of disabling Phlox, and then Phlox's ability will re-enable Li Nalas?
Or can Phlox's ability re-enable Li Nalas, who can then imediately Disable again to prevent Phlox from Disabling?

No. In the example given, if you use Phlox. Phlox must finish his card text, enabling all cards, before Li Nalas may disable to keep Phlox from disabling. Li Nalas will be disabled after Phlox’s card text has finished re-enabling all the cards on his ship.