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As long as the thread is through the nut, you should be fine. Extra thread does nothing to add strength. I do remember form my long distant apprenticeship days that minimum standard was 1/2 the diameter of the thread, ie., 1/4" on a 1/2 bolt. Make sure when you cut it to coat the end with something to prevent rust (grease works well if the bolt is somewhere you won't rub against it). I don't know how you plan on cutting it, but if it's a graded bolt, be careful not to get it too hot.
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