The green card rules would be a good basis on which to answer.
Your mother ship approaches and performs a hostile act - you can retaliate.
The mother ship then retires and poses no further threat to you or any vessel you are charged to protect - you can pursue and challenge but not engage.
The mother ship perceives your hot pursuit as a hostile act and attacks - you can retaliate.
The mother ship is disabled, on fire, and sinking - if they continue to engage you can continue to return fire. If they surrender then you cannot continue to engage and, when safe to do so, render assistance and take their surrender.
It then elects to re-attack the mother ship - aggressively so because the crew believe the ship still poses a threat, to themselves and others. Is that reasonable?
In this case they should not engage.
Now the Belgrano is a different matter.