Mergers, acquisitions, and other optimization activity can lead to a scenario where you want to merge multiple on-premises Skype for Business organizations into a single O365 Tenant, be that for Skype for Business Online or Teams.
Usually, the organization starts this process by synchronizing the on-prem AD contents from all organizations with Azure AD. This is followed by Exchange hybrid configuration. Both AD/AAD and Exchange support simultaneous hybrid configurations with multiple on-prem organizations.
Skype for Business, however, only permits one on-prem organization to be in a hybrid configuration at a time. The first organization is configured for hybrid, and the first SfBO or Teams users appear. Shortly after that, a report will come in to helpdesk about the online users not being able to reach the non-hybrid on-prem SfB organizations. Investigation shows that the on-prem users in the hybrid organizations can, however, reach these other organizations.
What’s going on can be a maddening process to unravel. For once, it’s not DNS or the network! When the AD/AAD sync is configured, the domain for the non-hybrid on-prem SfB organization is configured in the tenant (AD, Exchange, or a number of other reasons). This causes O365 to think that it now owns this domain for all O365 services, including SIP. The traffic to the user never leaves the hybrid organization via the federation processes, and results in a user not found scenario.
The solution is a simple one: Run the Disabled-CsOnlineSipDomain cmdlet against the non-hybrid on-prem SfB domain, from SfB online powershell. This tells O365 to ignore that domain for SIP purposes (but leave AD, Exchange, and others alone). Now the traffic will leave the organization and reach the intended user via federation. Problem solved!