I was only considering the conflict between the system-provided SQLite and the private copy of SQLite in your binary, since that seemed to be what your article was about, and is the most common conflict. I hadn't actually considered that you would actually statically link two copies of the same version (or even different versions) of SQLite into your own binary and use those two different copies of SQLite to open connections to the same exact file.

In any case, don't have two different versions (by versions I mean copies) of SQLite open the same file in the same process. This is because os_unix.c does deferred closing of fds based on refcounting the number of open connections to the same path. With multiple libraries opening connections to the same path, the refcount for that path won't be correct in either copy of the library.