upmostlyDo you even need a database?
You need databases if you need any kind of atomicity. Doing atomic writes is extremely fragile if you are just on top of the filesystem.
This is also why many databases have persistence issues and can easily corrupt on-disk data on crash. Rocksdb on windows is a very simple example a couple years back. It was regularly having corruption issues when doing development with it.
Honestly, at this point, if I had a design that required making atomic changes to files, I'd redo the design to use SQLite. The other way around sounds crazy to me.
"Why use spray paint when you can achieve the same effect by ejecting paint from your mouth in a uniform high-velocity mist?" If you happen to have developed that particular weird skill, by all means use it, but if you haven't, don't start now.
That probably sounds soft and lazy. I should learn to use my operating system's filesystem APIs safely. It would make me a better person. But honestly, I think that's a very niche skill these days, and you should consider if you really need it now and if you'll ever benefit from it in the future.
Also, even if you do it right, the people who inherit your code probably won't develop the same skills. They'll tell their boss it's impossibly dangerous to make any changes, and they'll replace it with a database.