The only thing that I would add to your procedure is:
(1) Make a duplicate, non-hidden copy of the hidden configuration file, and put it in a protected subdirectory of
(say ...) /root. Make this file read-only. Pick a file-name that is distinctive, including date, version-number and so on, 'cuz you're gonna keep this file forever.
(2) Rename the hidden file out of the way. Then, run
make distclean, which ordinarily would wipe out
that file. Then, rename it back. Now, you can be sure that subsequent
make steps will, indeed, recompile everything.
(It does not take long ...)
If you are very disciplined to keep
every config file ... even those that didn't work as you wanted them to(!) ... and if you also maintain a
"Captain's Log, Stardate 1234.5" with that same self-discipline, then you can use
diff to identify the complete set of changes between any configuration and any other. You can also revert to any previous configuration with absolute accuracy.
(I also know of some folks, with many different systems to maintain, who copy into a single backup-file per system, but they've set up the directory as a
git repo, allowing them to do
version control on the configurations. Another very good way to do it.)