Retina, 2323 22 bytes

Lms`^Lmsl`(.+)$(?=.+^\1$)
D`

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Lms`^Lmsl`(.+)$(?=.+^\1$)

List duplicated lines. The m modifier allows the ^ and $ to match the start and end of a line in the lookahead. The s modifier allows us to look ahead past newlines using just .+. The l modifier automatically anchors the match to whole lines. I can't use the p flag though as the match could be more than one line at once, however the next stage will deal with that.

D`

Deduplicate that list.