You have three choices when you need to remove a primary account from your profile.You can make a new profile (recommended), remove all Exchange accounts from your profile then add the new account back, or remove a key from the registry so you can delete the primary account from the registry.
You can edit the registry to remove the primary assignment, however it is not supported and not recommended by Microsoft.
If you mess up, you will need to make a new profile, restore the profile key you exported, or use System Restore to go back to a previous restore point. Press Windows key R to open the Run command then type regedit in the Run field and press Enter.
This step should not be necessary under normal circumstances.
In the time it took to read the previous paragraph Lync Server should have synchronized and outstanding changes in Active Directory and Step #2 can be manually processed.
if you have a lot of Exchange accounts or the mailboxes you are keeping in the profile are huge, you can edit the registry to remove the 'primary' flag then delete the account.
Editing the registry is generally the better option when the mailboxes will take a long time to re-sync (or you are on a metered connection) or if you have a lot of Exchange accounts in your profile.
When you move from one Microsoft Exchange service to another, such as from an internal Exchange server to Office365, and want to retain the current profile, you cannot remove the original Exchange account from your profile.
The primary Exchange account is the first account added to the profile.
The second half of the server-side process is controlled by the Address Book Service which pulls information from the SQL database and writes the changes to the address book files.
cmdlet is run then a ‘synchronize now‘ event is marked and the update is not actually run immediately.
The primary account cannot be removed from a profile until all other Exchange accounts are removed from the profile (when the primary is removed, the next Exchange account added is considered the primary).