Your alternating layers idea could work, you'd just need a Global Variable to keep track of the layer the trail sprites are spawned on and then you could have an event like this to clear them:
Conditions:
System->For Each Trail_Sprite
Trail_Sprite->Is on layer LAYER_VARIABLE
Actions:
Trail_Sprite->Destroy
Sub-Event:
Conditions:
System->Compare Variable->LAYER_VARIABLE = 1
Actions:
System->Set Value->LAYER_VARIABLE = 2
Else:
Actions:
System->Set Value->LAYER_VARIABLE = 1
An alternative to using different layers would be to give your trail sprites an alternating instance variable, the event to clear them would be pretty much the same but instead of checking what layer the sprites are on, you'd just check their instance variable