We upgraded to new servers twice up, once on a standalone environment and once from SharePoint integrated to standalone.
You are right, you have to deactivate the licence on the old server and activate on the new one. Ideally, you have an online connection to Webcon's licence server. If you have to use the offline way (as it happened to us in one case), coordinate with WEBCON support beforehand, so that they return the new activation file as soon as possible.
As a personal opinion, I would take the chance to move from SharePoint to standalone rather than continue in integrated mode and new SharePoint version.
It takes some preparation beforehand, but this can be done gradually.
In our case, the move to standalone went quite smoothly and we also upgraded to a newer WEBCON Version. Good to have Prod and Test environments...