Just re-played "take down the rigs" and the two secrets I need are still on this level. I have the same problem you do though.
I collected everything on hard, but was never credited as collecting these two. Now, when I run through on easy, the intel is there, and i go to pick it up, and no credit again.
Seeker counter still reads: 28 of 30.
If someone knows what the solution is, please help Mikhail and I out!