For me this is what happened:
- I never played this story back in 2013 when it was introduced
- I started Episode 1 on Tuesday, got to the point where I talked to the agent and got the green circles for the Diessa locations
- As a completionist I saw the [Optional] tag so I went first to Wayfarer and interacted with the first two encoded dead drop on the list (the two north one)
- Since I got only one point out of 12 in the Secret Contact achievement I thought I have to finish Diessa first so I went and finished the 6 Diessa dead drops
- At that point since the other reqs for moving on with the story in Diessa were already done the story moved on and the Encoded Dead Drops disappeared on both maps. I though no problem I'll replay later.
- So finished the story and started replaying
- Arrived to the part where I had to talk to the agent again, got the green circles in Diessa but no Encoded Dead Drops, so I tried to character logout and login
- the Encoded Dead Drops appeared in Diessa so I finished collecting those 6 and I was making sure the other req (helping Diessa events) was not done yet so the story stayed at that checkpoint, and went to Wayfarer
- There I didn't see the two north dead drops but was able to see and finish the other 5 down south, so now I am stuck with a 11/12 accomplishment in Secret Contact, but do not know which dead drop is missing since I cannot interact with the last two
- I tried everything I could to no avail
Hope this helps to track down the issue.