Warframe Reverts Alert Reward Lost

[Thairos]

I just completed an alert on Skyresh (phobos) for the shroud Nekros Helmet (Blueprint). Upon completion my warframe was reverted to a different warframe and weapons.  I checked my inventory and found no Shroud Nekros Helmet (blueprint).  It seems as though the alert/mission never happened but the planet no longer has the alert even though there is time remaining. Overall I have been noticing when changing warmframes and or weapons after completing the next mission everything is reverted back to a previous state.