I’m having the same issue. An example is this one: https://www.biorxiv.org/content/early/2018/02/07/261214
It’s an bioRxiv paper that’s been published in Neuron. I had the bioRxiv version already in the library, then when I tried to add the Neuron version, it says it’s already there…but with the bioRxiv info. Two papers, two DOIs but only one entry in the library possible…
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