I figured this one out, if you find the Class ID in IE Manage Add-ons like in the pic I have attached for Lync:
Then I created a bat file that deleted this key:
REG DELETE "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\Browser Helper Objects\{31D09BA0-12F5-4CCE-BE8A-2923E76605DA}"
REG DELETE "HKEY_CLASSES_ROOT\CLSID\{31D09BA0-12F5-4CCE-BE8A-2923E76605DA}" /f
And it was removed but they also say you might need to remove it from these keys as well but I didn't have too and of course Wow6432Node is for 64bit:
•HKEY_CLASSES_ROOT\Wow6432Node\CLSID\
•HKEY_LOCAL_MACHINE\SOFTWARE\Classes\Wow6432Node\CLSID\
•HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\Approved Extensions
•HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Ext\Settings\