To make sure that you never lose any custom settings after trashing preferences you can make a copy of your preference file (after you have all of your settings re-established) and use (a copy of) that "pristine" preference file to replace any future corrupt preference files you may have.
To find the preference file that you are making a copy of:
On Windows 7 and above the preference files are hidden. To find them go to the Control Panel and open Folder Options and then click the View tab. Then select “Show hidden files and folders” or “Show hidden files, folders or drive options” in Advanced Settings. The file you want to copy is the folder at the end of this path: C:\Users\[User Name]\AppData\Roaming\Adobe\Adobe Illustrator [version number].