That's interesting to hear. I wasn't expecting you to utilise much of the database system as much as you are.
When you delete traits it doesn't update the list, so unless you save the project there and then, it won't update the respective JSON files. Traits are considered separate data items compared to the characters themselves, as you've probably noticed.
Just bear in mind the changes being made to Story Creator... I will be updating the devlog where I will keep yourself and others up-to-date, but the database system you're used to is to be replaced as it's very niche and doesn't allow for any modifications. Not to mention the code has mostly been copied and pasted and not refactored the way it should be.
There were just too many problems with the codebase and I didn't think a lot of those things through at the time.
JSON files for saving data is not ideal for large projects and doesn't scale well, meaning that larger projects will take longer to load. So, ideally, I would migrate database functionality to an SQLite database for managing data with options to export the data to JSON format later if preferred.
If you want to keep the database options you have as they are, I will consider implementing "Mods" for this software in which everything that was there before can still be used, if you would prefer this.