I think I may have isolated my problem. My experimentation is with sockets and threads, it would seem that the threads I am creating and using the FTcpListener class are hanging around after the application is stopped (still running in the editor). As such I imagine it’s not possible for the Hot Reload to relink to the new DLLs due to currently active calls to the older DLLs.
Once I have untangled my mess and confirmed that hot-reload is working for me I will update this answer.
edit : After untangling the mess I had made with threads my project is now hot-loading happily. I had several threads knocking about that were not being stopped at the end of play, so they were living on in the Editor. This prevented the hot link from using the new code as well as undesired behaviour.
If anyone else is finding that hotlink is constantly using the previous version of code, might be worth checking that there isn’t some thread or something isn’t hanging about.