Are all of the defending players' ships that hyperspace out in this battle not considered destroyed (for score calculation) or is it just the ones that reach 1-2 of the assaulting team's edge that hyperspace out?

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If a ship that retreats is at distance 1-2 of the assaulting team's player edge when it is removed from the play area, the defending team gains a number of victory tokens equal to that ship's command value. That ship does not count as destroyed when determining score.

My reading of that is the second sentence follows the first, so only those ships which reach 1-2 of the assaulting team's edge don't count as being destroyed.

The Defending team's ships can declare a Hyperspace Retreat a round earlier than normal. If they survive to the start of the Status Phase are removed from play. If and only if they are at distance 1-2 when removed they don't count as destroyed for scoring, don't get scarred, and get Victory Tokens equal to their command value.

Defending team's ships that Hyperspace Retreat but don't make it to distance 1-2 count as destroyed for scoring, but don't get scarred (but don't give either side Victory Tokens).

The assaulting team's ships can Hyperspace Retreat starting Round 4 and, if they survive to the start of the Status Phase disappear, count as destroyed for scoring, but don't get scarred - same as normal.