Up until now, I've been using the convert tool in Emby server. You can select a whole library and convert it, or individual items/playlists/collections; with options to automatically convert new media as it's added.
Tbh, I've been having a bit of trouble with it re-converting media it's already done, so I was looking for another solution.
Someone in this thread mentioned tdarr, so I'm going to be looking into that this weekend. Seems like a much more manageable tool with more powerful options.
/edit; I should also mention, this is a long process. Using an rtx4080, it was almost 3 full months non-stop to convert my entire media library from mostly h264 -> h265.