Brad---Don't try to fight it, just go with it.
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Good point, because basically you probably won't have a choice.
When you consider that a very large percentage of rifles, particularly early rifles, have had the barrels cut back and the locks converted to percussion, when you find an unaltered one you better buy it!
I would think, only from my experience, that easily 80% of flint guns available today were altered. And many, most, of those have been reconverted, restored.
According to Dillin in his book, he laments that this has been going on at least as early as before 1900.
Keep in mind that here is no comparison in collecting Military guns where tens of thousands were produced, to Kentucky rifles who's production was a miniscule percentage of that. Sort of like collecting Toyota Camrys to Ferrari's!
Just my opinion of course, and your mileage may vary.