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A situation happened in a game recently and I was wonder how others would interpret it

The Thunderstrike rule for the Storm Speeder Thunderstrike reads as:

Thunderstrike: Each time this model has shot, select one enemy MONSTER or VEHICLE unit that was hit by one or more attacks made by this model this phase. Until the end of the phase, each time a friendly ADEPTUS ASTARTES unit makes a ranged attack that targets that enemy unit, add 1 to the Wound roll.

I targeted a unit that included a Carnifex lead by Old One Eye, the final attack was the Twin Icarus rocket pod. With its attacks it destroyed the Carnifex and put wounds on Old One Eye.
My question is that since I targeted and hit the attached unit of Carnifex and after destroying it Old One Eye became a separate unit is it still effected by the Thunderstike rule?

Yes; see the Design Commentary regarding Persistent Effects.