Multiple account Skype for business / Lync

To solve the problem, open your Skype configuration folder, usually it's /home/{your_home_folder}/.Skype/ and delete the shared.xml file found here.
After restarting Skype, it will be possible to login with Microsoft account.

It would be possible to run a macro from the command-line, using a batch script which inserts the log-in details into this secondary Skype session. You'd be able to incorporate /secondary within this script file.

This means that you won't be logged in on launch, but the script would go on to log you in automatically prior to the instance launch.

As for having the same account logged in and receiving live updates, in regard to if the first instance has read or seen a message and the second instance following its lead and updating without user interaction. It is to my belief that both the sessions will not work simultaneously in this way.

It goes without saying that there'd be potential security risks through having these details stored in such an open manner.

This article may hold details should you wish to pursue: http://www.ultraedit.com/support/tutorials_power_tips/ultraedit/run_macro_script_from_command_line.html