About moving files between packages, this was done by our beloved upstream. We try to track upstream closely, that's the whole point of the xorg-edgers project. For fool-proof packages, please stay with official distribution packages.
If upgrading development headers "breaks your entire system", you must have gotten out of sync. Just uninstall them all, they are not needed for normal usage. You can then reinstall them from the archive if you need to compile something.