Michael, you need to build from scratch. The values are set and tweaked in various phases of configure and then written to _sysconfigdata.py for installation.

The values in the file reflect the values used during the build, but many of them are not used in an installed version of Python.

Three important phases are:

1) Building modules in the tree during the build process.
2) In-tree testing of build module feature.
3) Building and installing modules with an installed version of Python.

The initial configuration scripts must match the location where the export files will be installed. And the _sysconfigdata.py definitions used to build external modules in an installed version of Python must refer to the proper location.

All of the pieces are interconnected and must be tested in a wholistic manner. A partial rebuild does not test the impact of the patch.