The Pro Tools updates for Pro Tools 10.3.6 onwards including 11 and 12 are designed to be in place updates meaning that they can be run over the top of a current installation most of the time these updates are successfully without any issue but as with any software on rare occasions problems may occur.
So at Pro Tools PC we have a standard guideline that we advise all users to follow which is as follows:
1) Create a system backup to an external or additional hard drive (not your Windows system drive) that can be easily restored if any major problem should occur and you need to roll back to your current "pre update" state, This is your safety net and a backup like this should be performed periodically anyway just as good working practice.
You can either use the "Windows System Backup & Restore" feature or use a 3rd party application such as Paragon Backup and Recovery (There is a Free edition that is perfectly adequate available here).
2) Use Trasher to backup your Pro Tools Preferences (these can be restore at a later date in case you have to uninstall and reinstall from scratch for any reason).
3) Download and install the desired update or use the Pro Tools update/application manager with Pro Tools 12 and install.
4) Restart the system and launch Pro Tools and everything should work as intended. If you run in to problems you can uninstall the current version of Pro Tools by going to the Windows Control Panel>Programs and Features. There you'll find the Pro Tools item in the list, Select it with your mouse cursor and then click the uninstall/change tab in the title bar of the window to uninstall.
5) once the process has completed you can again restart your system and now perform a cleanup of any files that may have been left behind by following this document.