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I'm not sure if this applies to all of the Jackdaws elite plans, but concerning the elite mortar plan; I found the location of this particular plan using a treasure map, and thus obtained the plan itself, BEFORE upgrading level 2 and 3 of the Mortars. Now that I have reached the point where I can upgrade the Mortars to maximum I cannot as I found the elite plan too early.
As I said; I have reached the point where I can upgrade the mortars to max, meaning I have already purchased level 2 and level 3. I have the materials and the elite plan yet the "prequisite: elite mortar plan" is in red meaning that I haven't got it, when I know that I have as I got it ages ago. Materials and funds are in gold colour meaning that I have them sufficent.
As you said you used a treasure map I can assume the chest you opened was buried and therefore not the elite mortar plans, as they are found in the Antocha Wreck directly below Nassau. I find it likely that you found the elite mortar STORAGE plans buried in Matanzas and were simply confused. As for the elite fire barrel storage plans, they, oddly, like the diamond sails, can only be obtained through Kenway's fleet.
Buried treasure does not count towards the completion of an area. Secrets are only composed of letters manuscripts and treasure maps. It will however say you have a treasure that corrosponds with the location you are in after loading or fast travel.