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Here's the mini-guide which I made for enemies and items:
Last appearance of Enemies that can be permanently missed.
Found before the encounters on the overworld change:- ~At Sea => 40:Killer Fish. 42:Helldiver. 45:Buccaneer. 52:Sea Snake. ~Palamecia Desert => 31:Antlion. 54:Land Ray. ~Land between Fynn & Palamecia Desert => 11:Phorusracos.
Found in Palamecia Castle:- 22:Skull. 71:Eyemoeba. 91:Black Knight. 94:Stone Golem. 106:General.
(Note: Half of these should appear fairly often and would be difficult to miss normally!)
Items which are possible to fully miss and their chest locations. Dreadnought: Sleep Blade, Dark bow, Main Gauche. Leviathan: Gaia Blade. Paul's House: Blood Sword. Cyclone: Ripper *, Defender *. Palamecia Castle: Sun Blade *.
* = Alternatively possible to get these from a limited enemy, or boss (as below).
Limited occurring enemies, with limited items (i.e. only a small number can be obtained elsewhere). Gottos: Ripper. Royal Guard: Poison Axe, Unicorn Horn. Black Knight: Sun Blade. General: Spider's Silk, Diamond Gloves, Rune Axe.
One time bosses, with limited items (i.e. only a small number can be obtained elsewhere): Emperor: Diamond Armour, Defender. Astaroth: White Robe, Spider's Silk. ---
Some of the low-lvl items are miss-able too. The only one I'm sure of is Mythril Knife, the only monster that drops it is Borgen. And once the world changes past a certain event, all of the old shops will be removed, leaving you unable to buy anymore of it (in a particular file I noticed it was the only item I am missing).
Not sure about the others, but it is very likely that some of the old items that the weapon/armor vendors sell are miss-able.