If you complete a Corpus Void Storm mission and recall back to your Railjack while still in your Necramech, the relic is not opened. In the linked video you can see I select a relic, complete a Void Storm exterminate with 10 reactant, recall to the Raijack while still in Necramech, and don't receive a relic reward. The relic is not spent, I still have the same amount after the mission is concluded.
I have reproduced this multiple times, first when I noticed it, and then twice more in testing.
NOTE: This is not a problem on Grineer Void Storm missions. I recalled from a destroyed missile platform while still in the Necramech, received the relic reward immediately upon returning to the Railjack in my Necramech.