Jean, you are certainly trying to dodge the obvious.
So after the author decoded C2, and it was fully explained to him, he experienced,
"no difficulty was apprehended in mastering the others;"
So Jean, what others if not C1 & C3?
"That they would attach no importance to a seemingly unintelligible writing seems quite natural; but their attention being called to them by the publication of this narrative, may result in eventually bringing to light the missing paper."
I don't know what school you went to, but the above is one sentence, not multiple sentences. The author has clearly identified what his readers will see to be an
"unintelligible writing" and in this same sentence he also clearly details that it is a
missing paper.

Hence=
missing unintelligible paper. 
One sentence providing a very clear statement about an unintelligible paper that is missing.
Dude, did you even go to school?
Another problem/trap you have manufactured for yourself is with the key, as he already has it which is why he was allegedly able to decode C2, so how does he know that there is another missing vital key or paper?

Can you say, "Ut-oh! Bigscoop just shined more of that annoying bright factual light in my secret dark corner!"
So without all of the dodging and weaving what were,
"the others that he had
no difficulty in mastering?"
And, can you explain
how the author knew about the missing paper and that it would appear unintelligible?
It's all clearly in the author's own words......so please, enlighten us.