I'm guessing you are using either the TC sawed flints or something similar with two pre cut angle surfaces. I'm pretty sure, with great care (eye/hand protection)a person could use a fixed grinder wheel to shave off one beveled edge thus allowing the new flat to slide closer to the lock flint screw and giving you plenty of frizzen clearance. This cannot be done with real black or yellow flints as they chip. Real flints come in all sizes and may be a better, safer, way to go for you. CVA mountain rifles use a small flint like a 5/8" size. TC flintlocks can use the pre sawed or 3/4" real flints. If you try to grind one edge, exterme caution and proper tools need to be utalized and you do so at some risk so this is not an endorsement of the above just something in my past was remembered. One more thought, a verticle fixed mount disk sander may also work. For those who will say this is too dangerous to try, most wood workers and metal fabricators have equal risks everyday using power tools and small objects and do it in a safe manner. The issue is safety.
I probably have 75 english black flints. These are by far the most used by traditional black powder shooters, The French yellows are a bit harder to get maybe spark slightly better than the english blacks. yellows are also somewhat black with yellow hues. Both are good for flintlocks and look cool too.
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