This came up the other day and Iwas unsure of how to handle it

A thunderhawk full of marines did a ground assault against one of my formations, as it assaults I overwatch at the thunderhawk (assumed here that overwatch hapens after the amrines disembark) destroying the thunderhawk. This creates three blast markers, Now as far as the assault is concerned the combined thunderhawk and marines are a single formation, hwoever the blast markers belong to the thunderhawk as that is what was shot at and if it had survived would have been the one with the blast markers follwing the assault, so what happens if the thunderhawk is destroyed by overwatch, I see three possible scenarios
1) the marines have no blast markers, when the thunderhawk dies it takes its blast markers with it, I am fairly sure that is wrong
2) The marine formation has three blast markers for the duration of the assault but then they are removed after the assualt when formations revert to separate entities, this is how we played it
3) The marines have three blast markers during the assault and keeep them afterwards as there is no mechanism for removing blast markers
Opions on which is the correct solution would be appreciated

I would say 2

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I'm going with 2 as well....but it's an odd situation for sure.

I thought overwatch could take place before or after a disembark move, but at the end of the transporting units move?

It can, but there is an exception for air assalt I believe, I think it was in an FAQ

Yep, a plane landing doesn't count as movement, so overwatch takes place after the disembarking, with the whole lot counting as one formation.

2. Most likely the SM formations would still end up with BMs from casualties during the assault, but the BMs on the Thawk would go with the now-dead Thawk.

As noted, the before/after disembark choice for OW fire only applies to ground transport, not Planetfall or Air Assault.

once the THwk activates, the infantry and it are single formation unil the end of the assault. any BMs acquired through AA or OW apply to the whole formation for the duration of the assault though they remain with the relevant formations post assault (or are removed with the dead formation), so #2 seems the correct solution.