Minor incongruence?

[Fyraltari]

They were looking for a goblin with crimson mantle.

That wasn't in question?

I'm fairly certain the goblins were only trying to capture Lirian's gate (maybe several times). Redcloak only learns of Lirian's gate through the knowledge from Crimson Mantle, and doesn't learn about the others until [events of SoD]. The "thwarted" you mentioned is referring to the Order of the Scribble, not the Sapphire Guard, if I recall correctly.

Redcloak also says that Kraagor "killed thousands of goblins when he was alive," which I'm assuming was before he died, thus it was before Soon formed the Sapphire Guard. That last bit might not back up or refute anything, it might just be me establishing a timeline.

Spoiler: SoD

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p43
Redcloak: But their efforts were thwarted, firstly by a band of adventurers -
Panel showing the Order of the Scribble (with a conspicuously absent Soo Kim) curbstomping a bunch of goblins, one of which is wearing the crimson Mantle, in a dungeon of some kind.
p44
Redcloak: -and years later by an order of paladins native to Azure City. The Crimson Mantle was passed down from cleric to cleric, though, so the quest continued.
Right-Eye:(That's why it's so tattered.)
Panel showing two Sapphire Guards killing goblins, one of which is wearing a never otherwise-seen purple cloak, on some kind of rock.

[Precure]

https://www.giantitp.com/comics/oots0277.html

Redcloak is referring to this event.

[Synesthesy]

There is neither a retcon nor a mistake: it is just written in a way that makes people who didn't read SoD understand everything. It is really important not to do anything that assumes free-users have bought something.

Spoiler

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as, for example, the revelation of Redcloak's plan with Tsukiko is a HUGE revelation if you didn't read SoD, while if you did, the revelation in SoD is HUGE, and you'll see in a really different way the conflict between Redcloak and Tsukiko. In other words, the scene is built to be good for both owners of SoD and free-users who are just reading a comic online

[Peelee]

My take on the reason is that somebody in the Sapphire Guard did a Divination or somesuch in the past and got a divine response along the lines ''Kill the goblin in red cloak, lest he conquers a Gate and ye all croak''.

Aye. They could have just visited the Oracle who told them that a red-cloaked goblin will be the harbinger of the Gate's destruction. None of the goblins need to know about Soon's Gate for that to be 100% true but misleading as all get-out, which also perfectly fits the Oracle's attitude towards humans.

[B. Dandelion]

We can't definitively rule out the possibility of there being a prophecy related to the Crimson Mantle being Azure City's destruction. But for it to have never come up in all this time would seem like a glaring omission, especially in HtPGHS.

Spoiler: HtPGHS

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Gin-Jun, who's obsessed with the Mantle, can never think to marshal the single most relevant argument for it being a threat? A definitive prophecy guaranteeing the destruction of Azure City obviously trumps a nebulous potential threat to the world. It should have weighed on his mind, and the minds of all the paladins.

[Manga Shoggoth]

I don't buy it. How can he decipher a diary just by knowing a location?

In addition to all the other answers, a known plaintext attack is a classic way of breaking a cipher.

How difficult this would be would depend on the encoding.

If only the co-ordinates were encoded, then knowing the location of Lirian's gate would be relatively easy.

If all the diary was encoded then you would have to look to see something that looked like planar co-ordinates.

If all the diary was encoded but had no format (or used different encoding at different times) the task would be correspondingly harder, but not for a lich with a high INT and lots of free time.