In my humble opinion, any development that needs this kind of detail should not use the amalgamation, but rather a checkout of a clone of the SQLite repository. That said, config.h can be safely removed, and recreated by running ./configure, which will fill in the platform specific details. `make sqlite.c` will build the amalgamation again. Besides, keeping a clone of the repository up to date instead of downloading the amalgamation for every release is network friendly.