If you ever happen to need to upgrade your SQLite version outside of a MacOS update it can be a little be unclear as to the next steps, at least it was for me. I was attempting to utilize Subversion (SVN) via the CLI to update a repository and every attempt to do so would fail with the below error:
svn: E200029: Couldn't perform atomic initialization
svn: E200030: SQLite compiled for 3.43.2, but running with 3.39.5
It was an extremely annoying error to navigate, especially after trying so many different approaches. I was able to resolve the issue by executing the following commands. Note: in my case I was using HomeBrew.
brew update
brew remove sqlite svn
brew reinstall sqlite svn --build-from-source
Once that is done if you execute sqlite3 --version
you should now see that you have the latest version installed and be able to utilize SVN.
Good luck!