Shots fired while Controlling the Mortar created by Engineer Elite Skill Mortar have no effect if the Mortar is evacuated while the shot is in the air; presumably, this also extends to shots in midair when the Mortar is destroyed.
Meanwhile, if a Mortar shot creates a field (such as the Ice Shot’s Chill effect), the field will have no effect unless someone is controlling the Mortar, but it does not require control throughout; if the Mortar is evacuated while the shot is in the air, then reclaimed while the field is extant, it will apply its effect.