There was an amnesty similar to what you're talking about in 1968 with the Gun Control Act, and it's the only firearms amnesty that's been offered.
The "Firearms Owners Protection Act" of 1986 (why is it that these bills always do the opposite of their title) did not have amnesty provisions. The big thing it did was ban civilian ownership of fully automatic firearms with specific exceptions where stringent requirements are met.
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If, in fact, what you're arguing is correct, then they must have added a serial number when registered.
The NFA requires all registered weapons to have a serial anyway, so I doubt what you're claiming happened.
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