perl -pi -e 's![\012\015]{1,2}!$/!g' file
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will not work right for mac->unix, mac->dos or unix->mac, because two consecutive \015 or \012 chars will be converted into single ones. So if you have blank lines, they'll get eaten. A safer alternative (though perhaps not an optimal RE) is:

perl -pi -e 's!(?:\015\012?|\012)!$/!g' file
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update: added safer alternative, made RE 17% faster