Thanks for bringing this to my attention, I have just raised a bug for this.
Just a quick note that upgrading from the web UI doesn't not have this effect, it only happens when upgrading from a terminal with apt upgrade, or from VMCentre (which uses this same method).
A quick fix in the meantime without needing to log on to the web UI will be to edit /opt/logonbox-wireguard/conf/hypersocket.properties and change the https.port back to what you need it.
Chris.