My general experience with TheBat! is that once you've created something (template, custom tag, etc.) deleting it is either very difficult or impossible.

This really sucks. I have experience the same problem with templates and tags, and just can't get rid of them. I think that problem is tied to the overall design philosophy, which isn't really user friendly. I use many modern apps for all sorts of tasks, and the general trend of modern UIs is to simplify customization via a unified interface and external text-based configurations (JSON, YAML, etc.). TheBat! uses lots of dialog windows to control settings, with some setting being accessible from multiple menus (and often not well integrated). I think that the whole settings system should be simplified by exposing all settings in human readable text files, which can be easily edited and manually backed up — instead of having monolithic backups that rely on binary settings in proprietary file formats.