In Exchange 2013 you have to edit the OWA web.config file to add the IM server and certificate that Exchange should use to connect to Skype for Business 2013 or Lync 2013. Exchange 2016 has changed how this is configured. Now you have to configure override settings for it and they are now stored in Active Directory. The advantage is that you don't have to go to each Exchange server to edit the OWA web.config and the settings are preserved over upgrades/updates.
You use the New-SettingOverride cmdlet and specify one for IMServerName and one for IMCertificateThumbprint. When you have multiple Exchange servers using different certificates to talk to Skype for Business/Lync you need a pair for each server. Below you'll find an example for 2 Exchange servers called mbx1 and mbx2. They both connect to the Skype for Business 2015 pool sfbpool1.contoso.dk.
New-SettingOverride SetIMServerNameMbx1 -Server mbx1 -Component OwaServer -Section IMSettings -Parameters @('IMServerName=sfbpool1.contoso.dk') -Reason "OWA IM config"
New-SettingOverride SetIMCertificateThumbprintMbx1 -Server mbx1 -Component OwaServer -Section IMSettings -Parameters @('IMCertificateThumbprint=F61D1F3922260B58C2AD779B7C6DDCAA69ECEC0F') -Reason "OWA IM Config"
New-SettingOverride SetIMServerNameMbx2 -Component OwaServer -Section IMSettings -Parameters @('IMServerName=sfbpool1.contoso.dk') -Reason "OWA IM config"
New-SettingOverride SetIMCertificateThumbprintMbx2 -Component OwaServer -Section IMSettings -Parameters @('IMCertificateThumbprint=A3B4AD7A6E5A21D05EFB1710A2788312C5BD2223') -Reason "OWA IM config"
Please note that it is only the use of OWA web.config that has changed in Exchange 2016. You still need to configure OWAMailboxPolicy and OWAVirtualDirectory as in Exchange 2013.