Hi,
The other card stays on top of the library. You're simultaneously shuffling the Nexus into the library and putting the other card on top of your library. Since this is happening at the same time, not one at at time, the card that you choose to keep on top of the library ends up on top of your shuffled library.
This is also confirmed on Magic Rules Manager Eli Shiffrin's Twitter:
https://twitter.com/EliShffrn/status/1050041800604303360Nathan Long
Magic Rules NetRep