Thank you for the report! ... hmm - this is exactly what happens already, though? If you don't deploy anything, or deploy only a little bit, and then retreat/lose the engagement, the enemy ships recover all (or most, if they had to do some actual fighting, as measured by whether they destroyed anything on the player's side) CR.
Am I missing some specific case where this doesn't work? I just tried it, and engaging an enemy fleet, waiting for them to deploy, and retreating (without deploying yourself) does not cause a CR loss for them.
(Is this vanilla or with mods, btw?)