Short version. There is a lot of difference between chert and flint. The long version follows. It is not scientific. It discusses the working properties of the various stones used for gunflints.
It is all the same thing, but the working properties are very different. Glass is an amorphous blob form with no real grain or structure of any kind beyond impurities or flow lines. It fractures very easily and has very poor working qualities for our purpose here. Flint is the next step up in toughness and structure. It is still pretty much an amorphous blob structure with flow lines and impurites being the real differences from lot to lot. It is just tough enough for the job, but it has a hidden advantage. As the materials get harder in this class, they break to less sharp edges. Flint still breaks to a very sharp fracture edge. Next you hit the Jaspers. These are highly impure forms that show the beginning of a microcrystaline form structure. The working properties are determined by the amount and type of impurity. They are pretty much not used as flints because they crumble rather than having a choncoidal fracture. Then we hit Chert. Chert is the true microcrystalline form of the Agates, but it is usually twisted and fractured thru out. Getting good solid pieces is hard to do. Flints made of good chert are halfway between flint and agate pretty much. They tend to still break or chip to a decent edge, and the good ones wear very well in the lock. Agate is the true microcrystalline form grown in cavities underground that get filled with super saturated water. The agate actually forms out of the solution. That is why so many agates are banded. It took many changes of the supersaturated solution to fill the cavity. Each carrying different impurities. Agate does not break to as sharp of an edge as flint does, and it is so tough that it tends to actually wear at the edge rather than chipping back. It still has the conchoidal fracture of the flints, but it takes many times the pressure that will remove a flake of flint to do anything with the agate. The clear agate off the Southwest "Fire Agates" is very tough durable material. The Clear filling material out of the Northwest "Thunder Eggs" is another source of very hard material. These agates are more pure and they are just downright tough. Quartz crystals are the true crystal form.
Chert can be several times tougher than any true flint. The fact that it still breaks to a decently sharp edge makes it about as high on the ladder as you can go without needing to grind a better edge on the material. There are exceptions to that, but not many. Put a thick leather glove on and strike a flake off a piece of Obsidian. You will get shards so sharp that cleanup is tough if you don't like to get cut! Do the same to flint and you get a fine edge, but nothing like the obsidian. Same as you move up the ladder. Chert takes a usable edge by flaking. Agate for the most part does not. (there are master knappers out there that can do very fine work in agate, but you can't afford their pieces for gunflints). The pertified woods produce some very tough durable flints if you grind an edge on them. Right now, I am using flints cut from a piece of petrified wood found on a sandbar along the Mississippi. The best I ever made were from what is called Bloodstone.
The perception that they are the same because they are made from the same base material is just simply wrong. They progress in hardness and toughness, with the toughest materail being many times tougher than the best flint. If Agate broke as sharp as flint does and flaked back from the edge like flint does, we would use nothing else! It doesn't! You have to grind an edge on agate and touch it up the same. Garnet also makes a very good gunflint. It fractures back from the strikes, in effect knapping itself as you use it. Gooid usable material is not easy to find tho!
