I am facing a similar issue with version 3.12.4 and earlier. I am not using the new Octopus built in certificate store. We have a wildcard cert that is bound to ('*'/' '/'0.0.0.0') port 443 for multiple websites. When changing an existing website IP Address binding from ('*'/' '/'0.0.0.0') in the "Deploy IIS Website" step, the "Removing unused SSL certificate binding" action is removing the cert binding from all websites; taking those sites down.
Thank you for taking the time to send through that PR, like I mentioned on GitHub we're working on a solution for your situation and the other scenarios customers had issues with. This fix is currently in review and should be ready to merge in the next day or so.
Yes, there is a plan to merge it! We've just been redirected to some bigger pieces of work that have taken priority. I'll make sure we get it reviewed early this week so it can be released in the next week or so.