Here is a patch, editing generatepress/inc/navigation.php
On line #98 in the item wrap I added
<li><a href="skype:user_profile?userinfo"><i class="fa fa-skype"></i></a></li> before the %3 parameter. A cleaner alternative is to create a custom nav walker. A negative is after each theme update I’ll have to update this file.
If you have any suggestions, just let me know.