When following the Challenge-Response credential programming on the first YubiKey, once you have clicked "Write Configuration", you will want to remove the first YubiKey, insert the second YubiKey, and click "Write Configuration" again. This will ensure the same credential is programmed into Slot 2 of each YubiKey. The software doesn't differentiate by YubiKey - it only cares about the credential, so you could program this same credential on 100+ YubiKeys and they would all work for Windows Login.
I'm assuming you've already figured out how to use the same YubiKey for multiple accounts. If not, you simply need to open YubiKey Logon Administration, insert one of the configured YubiKeys, select the user account from the dropdown, and click "Configure" (and it's a good idea to follow this with "Test"). Repeat this for any other accounts you want to add the YubiKey requirement to.
Just a quick disclaimer - for Windows Login, the "require user input (button press)" option must NOT be enabled, otherwise login will fail.
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