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I have two domains I have transferred and hosted with MS name-servers to 365.
The first domain runs share-point servers, the second is used for primary email and has custom DNS enteritis to point to a square space portal. When I try to log on to Lync using this second domain, as the user account has this set up as their log in, the user can not log on to Lync - this only works by using the first domain, but this does not match the users primary email.
From my understanding, you have added and verified two domains in Office 365. You set the first A domain for SharePoint Online and set the second B domain for Exchange Online and Lync Online. The users' account and email address all have been changed to be like USER@B domain.com, while they could not log in to Lync with the changed credentials.
Then I have a question here, when you say " this only works by using the first domain, but this does not match the users primary email." What do you mean by "the first domain", does it refer to "the first domain runs share-point server" or the original onmicrosoft.com domain? What is the meaning of "the users primary email"? Is the primary email as USER@B domain.com or USER@***.onmicrosoft.com?
Actually, from the time that user account being created, even if Exchange Online works, it normally takes some more time until you can log in to Lync.
If you still cannot log in to Lync, please try to manually configure Lync 2010 by following the steps below:
1.On the Lync 2010 sign-in screen, click the gear icon in the upper-right corner. This action opens the Options page.
2.On the Options page, next to the Sign-in address box, click Advanced.
3.In the Advanced Connection Settings dialog box, make sure that Manual Configuration is selected and that the values in the boxes are exactly as follows:
Internal server name or IP address: sipdir.online.lync.com:443
External server name or IP address: sipdir.online.lync.com:443
4.Click OK two times to return to the sign-in screen. Then, sign in.
Just checking in to see whether the information was helpful. Please let us know if you would like additional assistance.