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I think that they keep at least one of the pens for the future presidential libraries. Also as souvenirs for the sponsor(s) and co-sponsor(s) of the Bill. Etc. Probably put one in some vault in the Smithsonian or somewhere else should the Bill eventually become a major policy changer. Imagine the pen used to write the Gettysburg Address or that wrote/signed the Emancipation Proclamation.
President Clinton surely sensed it when he took two pens and signed the Act into law. The first pen was the same one used by President Eisenhower to sign the Federal Highway Act of 1956,