Will a new installation over the top of the existing installation reprogram my existing settings? Also, to be clear, I assume over the top means not to uninstall the existing game first.
No. Installing the full release, over the top of the existing installation will not change any of your settings. Not one.
Correct.
DO NOT REMOVE YOUR CURRENT GAME INSTALLATION (
yes, I meant to shout that).
It reset all my gun sights to defaults.
Let me guess. You allowed Oculus to do the update? There is no way to tell Oculus not to update those files. They see the file as being changed and they restore them.
We are going to have to find another way for those custom files to be installed without Oculus knowing about it.
Can you rerun the patch from the AH temp directory?
You can try, as it will not hurt anything, but chances are it will fail again. I would suggest making sure nothing is running on the desktop, shut down any anti-xxx software, and moving it off the SSD to a regular HD.
NOTE:
If you move it to an HD, from the SSD, be sure to run the game from the new location before running the patch or the patch program will not find the right game version to install over.